Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0AGC5
DateThu Jan 5 11:28:45 GMT 2012
Unique Job ID549fcccad7d4d96c

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1slyA_
Top template information
PDB header:glycosyltransferase
Chain: A: PDB Molecule:70-kda soluble lytic transglycosylase;
PDBTitle: complex of the 70-kda soluble lytic transglycosylase with2 bulgecin a
Confidence and coverage
Confidence:100.0% Coverage: 34%
174 residues ( 34% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
430 residues ( 83%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MKKLKINYLFIGILALLLAVALWPSIPWFGKADNRIAAIQARGELRVSTIHTPLTYNEIN
Secondary structure 

























SS confidence 



























































Disorder  ????

















?????????????
























Disorder confidence 



























































 
   .........70.........80.........90.........100.........110.........120
Sequence  GKPFGLDYELAKQFADYLGVKLKVTVRQNISQLFDDLDNGNADLLAAGLVYNSERVKNYQ
Secondary structure 


















SS confidence 



























































Disorder 



























































Disorder confidence 



























































 
   .........130.........140.........150.........160.........170.........180
Sequence  PGPTYYSVSQQLVYKVGQYRPRTLGNLTAEQLTVAPGHVVVNDLQTLKETKFPELSWKVD
Secondary structure 


























SS confidence 



























































Disorder 


















????

























?????





Disorder confidence 



























































 
   .........190.........200.........210.........220.........230.........240
Sequence  DKKGSAELMEDVIEGKLDYTIADSVAISLFQRVHPELAVALDITDEQPVTWFSPLDGDNT
Secondary structure 






















SS confidence 



























































Disorder 



























































Disorder confidence 



























































 
   .........250.........260.........270.........280.........290.........300
Sequence  LSAALLDFFNEMNEDGTLARIEEKYLGHGDDFDYVDTRTFLRAVDAVLPQLKPLFEKYAE
Secondary structure 








SS confidence 



























































Disorder 

























?????????????????????












Disorder confidence 



























































 
   .........310.........320.........330.........340.........350.........360
Sequence  EIDWRLLAAIAYQESHWDAQATSPTGVRGMMMLTKNTAQSLGITDRTDAEQSISGGVRYL
Secondary structure 



























SS confidence 



























































Disorder 



























































Disorder confidence 



























































 
   .........370.........380.........390.........400.........410.........420
Sequence  QDMMSKVPESVPENERIWFALAAYNMGYAHMLDARALTAKTKGNPDSWADVKQRLPLLSQ
Secondary structure 



















SS confidence 



























































Disorder 







?






























??

??













Disorder confidence 



























































 
   .........430.........440.........450.........460.........470.........480
Sequence  KPYYSKLTYGYARGHEAYAYVENIRKYQISLVGYLQEKEKQATEAAMQLAQDYPAVSPTE
Secondary structure 



















SS confidence 



























































Disorder  ??































???????





?????????????
Disorder confidence 



























































 
   .........490.........500.........510........
Sequence  LGKEKFPFLSFLSQSSSNYLTHSPSLLFSRKGSEEKQN
Secondary structure 






















SS confidence 





































Disorder  ???????????????????????
??????????????
Disorder confidence 





































 

Confidence Key
High(9)                    Low (0)
?Disordered
Alpha helix
Beta strand

Domain analysis 

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

RankAligned region

PDB 1sly chain A

3D model

Region: 258 - 458
Aligned: 174
Modelled: 184
Confidence: 100.0%
Identity: 26%
PDB header:glycosyltransferase
Chain: A: PDB Molecule:70-kda soluble lytic transglycosylase;
PDBTitle: complex of the 70-kda soluble lytic transglycosylase with2 bulgecin a

Phyre2

PDB 2y8p chain A

3D model

Region: 271 - 454
Aligned: 174
Modelled: 184
Confidence: 100.0%
Identity: 19%
PDB header:lyase
Chain: A: PDB Molecule:endo-type membrane-bound lytic murein transglycosylase a;
PDBTitle: crystal structure of an outer membrane-anchored endolytic2 peptidoglycan lytic transglycosylase (mlte) from3 escherichia coli

Phyre2

PDB 2yln chain A

3D model

Region: 30 - 269
Aligned: 230
Modelled: 232
Confidence: 100.0%
Identity: 19%
PDB header:transport protein
Chain: A: PDB Molecule:putative abc transporter, periplasmic binding protein,
PDBTitle: crystal structure of the l-cystine solute receptor of2 neisseria gonorrhoeae in the closed conformation

Phyre2

PDB 3k4u chain A

3D model

Region: 42 - 274
Aligned: 227
Modelled: 232
Confidence: 100.0%
Identity: 24%
PDB header:transport protein
Chain: A: PDB Molecule:binding component of abc transporter;
PDBTitle: crystal structure of putative binding component of abc transporter2 from wolinella succinogenes dsm 1740 complexed with lysine

Phyre2

PDB 2a5s chain A domain 1

3D model

Region: 39 - 267
Aligned: 225
Modelled: 229
Confidence: 100.0%
Identity: 10%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 3hv1 chain A

3D model

Region: 29 - 278
Aligned: 247
Modelled: 250
Confidence: 100.0%
Identity: 17%
PDB header:transport protein
Chain: A: PDB Molecule:polar amino acid abc uptake transporter substrate
PDBTitle: crystal structure of a polar amino acid abc uptake2 transporter substrate binding protein from streptococcus3 thermophilus

Phyre2

PDB 2iee chain B

3D model

Region: 36 - 280
Aligned: 236
Modelled: 245
Confidence: 100.0%
Identity: 15%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:probable abc transporter extracellular-binding
PDBTitle: crystal structure of yckb_bacsu from bacillus subtilis.2 northeast structural genomics consortium target sr574.

Phyre2

PDB 2q89 chain A

3D model

Region: 31 - 267
Aligned: 231
Modelled: 232
Confidence: 100.0%
Identity: 17%
PDB header:transport protein
Chain: A: PDB Molecule:putative abc transporter amino acid-binding protein;
PDBTitle: crystal structure of ehub in complex with hydroxyectoine

Phyre2

PDB 3kbr chain A

3D model

Region: 33 - 266
Aligned: 226
Modelled: 234
Confidence: 100.0%
Identity: 21%
PDB header:lyase
Chain: A: PDB Molecule:cyclohexadienyl dehydratase;
PDBTitle: the crystal structure of cyclohexadienyl dehydratase precursor from2 pseudomonas aeruginosa pa01

Phyre2

PDB 1qsa chain A domain 2

3D model

Region: 290 - 458
Aligned: 142
Modelled: 152
Confidence: 100.0%
Identity: 31%
Fold: Lysozyme-like
Superfamily: Lysozyme-like
Family: Bacterial muramidase, catalytic domain

Phyre2

PDB 2rc9 chain A

3D model

Region: 51 - 267
Aligned: 213
Modelled: 217
Confidence: 100.0%
Identity: 11%
PDB header:membrane protein
Chain: A: PDB Molecule:glutamate [nmda] receptor subunit 3a;
PDBTitle: crystal structure of the nr3a ligand binding core complex with acpc at2 1.96 angstrom resolution

Phyre2

PDB 3kzg chain B

3D model

Region: 44 - 266
Aligned: 214
Modelled: 223
Confidence: 100.0%
Identity: 18%
PDB header:transport protein
Chain: B: PDB Molecule:arginine 3rd transport system periplasmic binding
PDBTitle: crystal structure of an arginine 3rd transport system2 periplasmic binding protein from legionella pneumophila

Phyre2

PDB 1pb7 chain A

3D model

Region: 39 - 267
Aligned: 227
Modelled: 229
Confidence: 100.0%
Identity: 16%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 3r39 chain A

3D model

Region: 39 - 267
Aligned: 225
Modelled: 227
Confidence: 100.0%
Identity: 18%
PDB header:transport protein
Chain: A: PDB Molecule:putative periplasmic binding protein;
PDBTitle: crystal structure of periplasmic d-alanine abc transporter from2 salmonella enterica

Phyre2

PDB 2vha chain B

3D model

Region: 29 - 268
Aligned: 235
Modelled: 238
Confidence: 100.0%
Identity: 15%
PDB header:transport protein
Chain: B: PDB Molecule:periplasmic binding transport protein;
PDBTitle: debp

Phyre2

PDB 2o1m chain B

3D model

Region: 41 - 267
Aligned: 218
Modelled: 227
Confidence: 100.0%
Identity: 20%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:probable amino-acid abc transporter
PDBTitle: crystal structure of the probable amino-acid abc2 transporter extracellular-binding protein ytmk from3 bacillus subtilis. northeast structural genomics4 consortium target sr572

Phyre2

PDB 1hsl chain A

3D model

Region: 43 - 267
Aligned: 219
Modelled: 224
Confidence: 100.0%
Identity: 21%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 3i6v chain A

3D model

Region: 44 - 267
Aligned: 208
Modelled: 214
Confidence: 100.0%
Identity: 17%
PDB header:transport protein
Chain: A: PDB Molecule:periplasmic his/glu/gln/arg/opine family-binding protein;
PDBTitle: crystal structure of a periplasmic his/glu/gln/arg/opine family-2 binding protein from silicibacter pomeroyi in complex with lysine

Phyre2

PDB 1lst chain A

3D model

Region: 43 - 269
Aligned: 221
Modelled: 222
Confidence: 100.0%
Identity: 21%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2

PDB 3g41 chain A

3D model

Region: 41 - 267
Aligned: 219
Modelled: 226
Confidence: 100.0%
Identity: 17%
PDB header:transport protein
Chain: A: PDB Molecule:amino acid abc transporter, periplasmic amino acid-binding
PDBTitle: the structure of cpn0482, the arginine binding protein from the2 periplasm of chlamydia pneumoniae

Phyre2
1

c1slyA_
2

c2y8pA_
3

c2ylnA_
4

c3k4uA_
5

d2a5sa1
6

c3hv1A_
7

c2ieeB_
8

c2q89A_
9

c3kbrA_
10

d1qsaa2
11

c2rc9A_
12

c3kzgB_
13

d1pb7a_
14

c3r39A_
15

c2vhaB_
16

c2o1mB_
17

d1hsla_
18

c3i6vA_
19

d1lsta_
20

c3g41A_
21



22



23



24



25



26



27



28



29



30



31



32



33



34



35



36



37



38



39



40



41



42



43



44



45



46



47



48



49



50



51



52



53



54



55



56



57



58



59



60



61



62



63



64



65



66



67



68



69



70



71



72



73



74



75



76



77



78



79



80



81



82



83



84



85



86



87



88



89



90



91



92



93



94



95



96



97



98



99



100



101



102



103



104



105



106



107



108



109



110



111



112



113



114



115



116



117



118



119



120



121



122



123



124



125



126



127



128



129



130



131



132



133



134



135



136



137



138



139



140



141



142



143



144



145



146



147



148



149



150



151



152



153



154



155



156



157



158



159



160



161



162



163



164



165



166



167



168



169



170



171



172



173



174



175



176



177



178



179



180



181



182



183



184



185



186



187



188



189



190



191



192



193



194



195



196



197



198



199



200



201



202



203



204



205



206



207



208



209



210



211



212



213



214



215



216



217



218



219



220



221



222



223



224



225



226



227



228



229



230



231



232



233






Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1slyA_



100.0 26 PDB header:glycosyltransferase
Chain: A: PDB Molecule:70-kda soluble lytic transglycosylase;
PDBTitle: complex of the 70-kda soluble lytic transglycosylase with2 bulgecin a
2c2y8pA_



100.0 19 PDB header:lyase
Chain: A: PDB Molecule:endo-type membrane-bound lytic murein transglycosylase a;
PDBTitle: crystal structure of an outer membrane-anchored endolytic2 peptidoglycan lytic transglycosylase (mlte) from3 escherichia coli
3c2ylnA_



100.0 19 PDB header:transport protein
Chain: A: PDB Molecule:putative abc transporter, periplasmic binding protein,
PDBTitle: crystal structure of the l-cystine solute receptor of2 neisseria gonorrhoeae in the closed conformation
4c3k4uA_



100.0 24 PDB header:transport protein
Chain: A: PDB Molecule:binding component of abc transporter;
PDBTitle: crystal structure of putative binding component of abc transporter2 from wolinella succinogenes dsm 1740 complexed with lysine
5d2a5sa1



100.0 10 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
6c3hv1A_



100.0 17 PDB header:transport protein
Chain: A: PDB Molecule:polar amino acid abc uptake transporter substrate
PDBTitle: crystal structure of a polar amino acid abc uptake2 transporter substrate binding protein from streptococcus3 thermophilus
7c2ieeB_



100.0 15 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:probable abc transporter extracellular-binding
PDBTitle: crystal structure of yckb_bacsu from bacillus subtilis.2 northeast structural genomics consortium target sr574.
8c2q89A_



100.0 17 PDB header:transport protein
Chain: A: PDB Molecule:putative abc transporter amino acid-binding protein;
PDBTitle: crystal structure of ehub in complex with hydroxyectoine
9c3kbrA_



100.0 21 PDB header:lyase
Chain: A: PDB Molecule:cyclohexadienyl dehydratase;
PDBTitle: the crystal structure of cyclohexadienyl dehydratase precursor from2 pseudomonas aeruginosa pa01
10d1qsaa2



100.0 31 Fold:Lysozyme-like
Superfamily:Lysozyme-like
Family:Bacterial muramidase, catalytic domain
11c2rc9A_



100.0 11 PDB header:membrane protein
Chain: A: PDB Molecule:glutamate [nmda] receptor subunit 3a;
PDBTitle: crystal structure of the nr3a ligand binding core complex with acpc at2 1.96 angstrom resolution
12c3kzgB_



100.0 18 PDB header:transport protein
Chain: B: PDB Molecule:arginine 3rd transport system periplasmic binding
PDBTitle: crystal structure of an arginine 3rd transport system2 periplasmic binding protein from legionella pneumophila
13d1pb7a_



100.0 16 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
14c3r39A_



100.0 18 PDB header:transport protein
Chain: A: PDB Molecule:putative periplasmic binding protein;
PDBTitle: crystal structure of periplasmic d-alanine abc transporter from2 salmonella enterica
15c2vhaB_



100.0 15 PDB header:transport protein
Chain: B: PDB Molecule:periplasmic binding transport protein;
PDBTitle: debp
16c2o1mB_



100.0 20 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:probable amino-acid abc transporter
PDBTitle: crystal structure of the probable amino-acid abc2 transporter extracellular-binding protein ytmk from3 bacillus subtilis. northeast structural genomics4 consortium target sr572
17d1hsla_



100.0 21 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
18c3i6vA_



100.0 17 PDB header:transport protein
Chain: A: PDB Molecule:periplasmic his/glu/gln/arg/opine family-binding protein;
PDBTitle: crystal structure of a periplasmic his/glu/gln/arg/opine family-2 binding protein from silicibacter pomeroyi in complex with lysine
19d1lsta_



100.0 21 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
20c3g41A_



100.0 17 PDB header:transport protein
Chain: A: PDB Molecule:amino acid abc transporter, periplasmic amino acid-binding
PDBTitle: the structure of cpn0482, the arginine binding protein from the2 periplasm of chlamydia pneumoniae
21c2q2aD_



not modelled 100.0 18 PDB header:transport protein
Chain: D: PDB Molecule:artj;
PDBTitle: crystal structures of the arginine-, lysine-, histidine-2 binding protein artj from the thermophilic bacterium3 geobacillus stearothermophilus
22c3h7mA_



not modelled 100.0 19 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of a histidine kinase sensor domain with2 similarity to periplasmic binding proteins
23c2v25B_



not modelled 100.0 17 PDB header:receptor
Chain: B: PDB Molecule:major cell-binding factor;
PDBTitle: structure of the campylobacter jejuni antigen peb1a, an2 aspartate and glutamate receptor with bound aspartate
24c2y7iB_



not modelled 100.0 15 PDB header:arginine-binding protein
Chain: B: PDB Molecule:stm4351;
PDBTitle: structural basis for high arginine specificity in salmonella2 typhimurium periplasmic binding protein stm4351.
25c3delC_



not modelled 100.0 19 PDB header:protein binding, transport protein
Chain: C: PDB Molecule:arginine binding protein;
PDBTitle: the structure of ct381, the arginine binding protein from the2 periplasm chlamydia trachomatis
26c1xt8B_



not modelled 100.0 16 PDB header:transport protein
Chain: B: PDB Molecule:putative amino-acid transporter periplasmic solute-binding
PDBTitle: crystal structure of cysteine-binding protein from campylobacter2 jejuni at 2.0 a resolution
27d1wdna_



not modelled 100.0 20 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
28c3mplA_



not modelled 100.0 16 PDB header:signaling protein
Chain: A: PDB Molecule:virulence sensor protein bvgs;
PDBTitle: crystal structure of bordetella pertussis bvgs vft2 domain (double2 mutant f375e/q461e)
29d1gbsa_



not modelled 100.0 20 Fold:Lysozyme-like
Superfamily:Lysozyme-like
Family:G-type lysozyme
30d1mqia_



not modelled 100.0 19 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
31c2yjpB_



not modelled 100.0 21 PDB header:transport protein
Chain: B: PDB Molecule:putative abc transporter, periplasmic binding protein,
PDBTitle: crystal structure of the solute receptors for l-cysteine of2 neisseria gonorrhoeae
32c3mgwA_



not modelled 100.0 21 PDB header:hydrolase
Chain: A: PDB Molecule:lysozyme g;
PDBTitle: thermodynamics and structure of a salmon cold-active goose-type2 lysozyme
33d1xt8a1



not modelled 100.0 16 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
34c2pyyB_



not modelled 100.0 15 PDB header:transport protein
Chain: B: PDB Molecule:ionotropic glutamate receptor bacterial homologue;
PDBTitle: crystal structure of the glur0 ligand-binding core from nostoc2 punctiforme in complex with (l)-glutamate
35d1s50a1



not modelled 100.0 16 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
36d1ii5a_



not modelled 100.0 16 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
37c2xx7B_



not modelled 99.9 19 PDB header:transport protein
Chain: B: PDB Molecule:glutamate receptor 2;
PDBTitle: crystal structure of 1-(4-(1-pyrrolidinylcarbonyl)phenyl)-3-2 (trifluoromethyl)-4,5,6,7-tetrahydro-1h-indazole in complex with3 the ligand binding domain of the rat glua2 receptor and glutamate4 at 2.2a resolution.
38c3gxkB_



not modelled 99.9 19 PDB header:hydrolase
Chain: B: PDB Molecule:goose-type lysozyme 1;
PDBTitle: the crystal structure of g-type lysozyme from atlantic cod2 (gadus morhua l.) in complex with nag oligomers sheds new3 light on substrate binding and the catalytic mechanism.4 native structure to 1.9
39d2f34a1



not modelled 99.9 18 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
40c2v3tA_



not modelled 99.9 12 PDB header:receptor
Chain: A: PDB Molecule:glutamate receptor delta-2 subunit synonym
PDBTitle: structure of the ligand-binding core of the ionotropic2 glutamate receptor-like glurdelta2 in the apo form
41c1yaeB_



not modelled 99.9 16 PDB header:membrane protein
Chain: B: PDB Molecule:glutamate receptor, ionotropic kainate 2;
PDBTitle: structure of the kainate receptor subunit glur6 agonist binding domain2 complexed with domoic acid
42c3kg2A_



not modelled 99.9 17 PDB header:membrane protein, transport protein
Chain: A: PDB Molecule:glutamate receptor 2;
PDBTitle: ampa subtype ionotropic glutamate receptor in complex with competitive2 antagonist zk 200775
43c3n5lA_



not modelled 99.3 12 PDB header:transport protein
Chain: A: PDB Molecule:binding protein component of abc phosphonate transporter;
PDBTitle: crystal structure of a binding protein component of abc phosphonate2 transporter (pa3383) from pseudomonas aeruginosa at 1.97 a resolution
44c2x26A_



not modelled 99.2 12 PDB header:transport protein
Chain: A: PDB Molecule:periplasmic aliphatic sulphonates-binding protein;
PDBTitle: crystal structure of the periplasmic aliphatic sulphonate2 binding protein ssua from escherichia coli
45c3e4rA_



not modelled 99.1 13 PDB header:transport protein
Chain: A: PDB Molecule:nitrate transport protein;
PDBTitle: crystal structure of the alkanesulfonate binding protein2 (ssua) from the phytopathogenic bacteria xanthomonas3 axonopodis pv. citri bound to hepes
46c3qslA_



not modelled 99.1 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative exported protein;
PDBTitle: structure of cae31940 from bordetella bronchiseptica rb50
47c3uifA_



not modelled 99.1 8 PDB header:transport protein
Chain: A: PDB Molecule:sulfonate abc transporter, periplasmic sulfonate-binding
PDBTitle: crystal structure of putative sulfonate abc transporter, periplasmic2 sulfonate-binding protein ssua from methylobacillus flagellatus kt
48c3hn0A_



not modelled 99.0 12 PDB header:transport protein
Chain: A: PDB Molecule:nitrate transport protein;
PDBTitle: crystal structure of an abc transporter (bdi_1369) from2 parabacteroides distasonis at 1.75 a resolution
49c3ix1A_



not modelled 98.9 11 PDB header:biosynthetic protein
Chain: A: PDB Molecule:n-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding
PDBTitle: periplasmic n-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding2 protein from bacillus halodurans
50c3ix1B_



not modelled 98.9 11 PDB header:biosynthetic protein
Chain: B: PDB Molecule:n-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding
PDBTitle: periplasmic n-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding2 protein from bacillus halodurans
51c2x7pA_



not modelled 98.9 12 PDB header:unknown function
Chain: A: PDB Molecule:possible thiamine biosynthesis enzyme;
PDBTitle: the conserved candida albicans ca3427 gene product defines a new2 family of proteins exhibiting the generic periplasmic binding3 protein structural fold
52c3un6A_



not modelled 98.9 11 PDB header:unknown function
Chain: A: PDB Molecule:hypothetical protein saouhsc_00137;
PDBTitle: 2.0 angstrom crystal structure of ligand binding component of abc-type2 import system from staphylococcus aureus with zinc bound
53c3gxaA_



not modelled 98.9 9 PDB header:protein binding
Chain: A: PDB Molecule:outer membrane lipoprotein gna1946;
PDBTitle: crystal structure of gna1946
54c3k2dA_



not modelled 98.8 11 PDB header:immune system
Chain: A: PDB Molecule:abc-type metal ion transport system, periplasmic component;
PDBTitle: crystal structure of immunogenic lipoprotein a from vibrio vulnificus
55c3ir1F_



not modelled 98.8 9 PDB header:protein binding
Chain: F: PDB Molecule:outer membrane lipoprotein gna1946;
PDBTitle: crystal structure of lipoprotein gna1946 from neisseria2 meningitidis
56d1qusa_



not modelled 98.8 15 Fold:Lysozyme-like
Superfamily:Lysozyme-like
Family:Bacterial muramidase, catalytic domain
57d1xs5a_



not modelled 98.7 8 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
58c3tqwA_



not modelled 98.7 14 PDB header:transport protein
Chain: A: PDB Molecule:methionine-binding protein;
PDBTitle: structure of a abc transporter, periplasmic substrate-binding protein2 from coxiella burnetii
59c3tmgA_



not modelled 98.6 11 PDB header:transport protein
Chain: A: PDB Molecule:glycine betaine, l-proline abc transporter,
PDBTitle: crystal structure of glycine betaine, l-proline abc transporter,2 glycine/betaine/l-proline-binding protein (prox) from borrelia3 burgdorferi
60c3l6gA_



not modelled 98.6 12 PDB header:glycine betaine-binding protein
Chain: A: PDB Molecule:betaine abc transporter permease and substrate binding
PDBTitle: crystal structure of lactococcal opuac in its open conformation
61d1us5a_



not modelled 98.3 12 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
62c2g29A_



not modelled 98.3 12 PDB header:transport protein
Chain: A: PDB Molecule:nitrate transport protein nrta;
PDBTitle: crystal structure of the periplasmic nitrate-binding2 protein nrta from synechocystis pcc 6803
63d1p99a_



not modelled 98.2 7 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
64c1p99A_



not modelled 98.2 7 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein pg110;
PDBTitle: 1.7a crystal structure of protein pg110 from staphylococcus2 aureus
65c3bkhA_



not modelled 98.2 19 PDB header:hydrolase
Chain: A: PDB Molecule:lytic transglycosylase;
PDBTitle: crystal structure of the bacteriophage phikz lytic2 transglycosylase, gp144
66c2qpqC_



not modelled 98.2 14 PDB header:transport protein
Chain: C: PDB Molecule:protein bug27;
PDBTitle: structure of bug27 from bordetella pertussis
67c2de4B_



not modelled 98.2 15 PDB header:hydrolase
Chain: B: PDB Molecule:dibenzothiophene desulfurization enzyme b;
PDBTitle: crystal structure of dszb c27s mutant in complex with biphenyl-2-2 sulfinic acid
68c3b50A_



not modelled 98.1 11 PDB header:transport protein
Chain: A: PDB Molecule:sialic acid-binding periplasmic protein siap;
PDBTitle: structure of h. influenzae sialic acid binding protein2 bound to neu5ac.
69c2f5xC_



not modelled 98.0 16 PDB header:transport protein
Chain: C: PDB Molecule:bugd;
PDBTitle: structure of periplasmic binding protein bugd
70c2dvzA_



not modelled 97.9 12 PDB header:transport protein
Chain: A: PDB Molecule:putative exported protein;
PDBTitle: structure of a periplasmic transporter
71c2pfzA_



not modelled 97.9 14 PDB header:transport protein
Chain: A: PDB Molecule:putative exported protein;
PDBTitle: crystal structure of dctp6, a bordetella pertussis2 extracytoplasmic solute receptor binding pyroglutamic acid
72c2i4cA_



not modelled 97.9 11 PDB header:transport protein
Chain: A: PDB Molecule:bicarbonate transporter;
PDBTitle: crystal structure of bicarbonate transport protein cmpa from2 synechocystis sp. pcc 6803 in complex with bicarbonate and calcium
73d1zbma1



not modelled 97.9 12 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
74c2vpnB_



not modelled 97.8 7 PDB header:transport
Chain: B: PDB Molecule:periplasmic substrate binding protein;
PDBTitle: high-resolution structure of the periplasmic ectoine-2 binding protein from teaabc trap-transporter of halomonas3 elongata
75d2czla1



not modelled 97.8 14 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
76c3gyyC_



not modelled 97.8 7 PDB header:transport protein
Chain: C: PDB Molecule:periplasmic substrate binding protein;
PDBTitle: the ectoine binding protein of the teaabc trap transporter teaa in the2 apo-state
77d1amfa_



not modelled 97.8 17 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
78c2zzxD_



not modelled 97.7 16 PDB header:transport protein
Chain: D: PDB Molecule:abc transporter, solute-binding protein;
PDBTitle: crystal structure of a periplasmic substrate binding protein in2 complex with lactate
79c3fxbB_



not modelled 97.7 10 PDB header:transport protein
Chain: B: PDB Molecule:trap dicarboxylate transporter, dctp subunit;
PDBTitle: crystal structure of the ectoine-binding protein ueha
80c3muqB_



not modelled 97.7 12 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized conserved protein;
PDBTitle: the crystal structure of a conserved functionally unknown protein from2 vibrio parahaemolyticus rimd 2210633
81c3fd3A_



not modelled 97.7 8 PDB header:transcription regulator
Chain: A: PDB Molecule:chromosome replication initiation inhibitor protein;
PDBTitle: structure of the c-terminal domains of a lysr family protein from2 agrobacterium tumefaciens str. c58.
82c2hpgB_



not modelled 97.7 12 PDB header:ligand binding protein
Chain: B: PDB Molecule:abc transporter, periplasmic substrate-binding
PDBTitle: the crystal structure of a thermophilic trap periplasmic2 binding protein
83c2pfyA_



not modelled 97.7 10 PDB header:transport protein
Chain: A: PDB Molecule:putative exported protein;
PDBTitle: crystal structure of dctp7, a bordetella pertussis2 extracytoplasmic solute receptor binding pyroglutamic acid
84c2ql3G_



not modelled 97.6 11 PDB header:transcription
Chain: G: PDB Molecule:probable transcriptional regulator, lysr family protein;
PDBTitle: crystal structure of the c-terminal domain of a probable lysr family2 transcriptional regulator from rhodococcus sp. rha1
85d1atga_



not modelled 97.6 14 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
86c2h5yC_



not modelled 97.6 14 PDB header:metal transport
Chain: C: PDB Molecule:molybdate-binding periplasmic protein;
PDBTitle: crystallographic structure of the molybdate-binding protein of2 xanthomonas citri at 1.7 ang resolution bound to molybdate
87c3n6uA_



not modelled 97.4 10 PDB header:transcription regulator
Chain: A: PDB Molecule:lysr type regulator of tsambcd;
PDBTitle: effector binding domain of tsar in complex with its inducer p-2 toluenesulfonate
88d2fyia1



not modelled 97.4 16 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
89c2rejA_



not modelled 97.4 13 PDB header:choline-binding protein
Chain: A: PDB Molecule:putative glycine betaine abc transporter protein;
PDBTitle: abc-transporter choline binding protein in unliganded semi-2 closed conformation
90d2esna2



not modelled 97.3 13 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
91c2hxrA_



not modelled 97.3 15 PDB header:transcription
Chain: A: PDB Molecule:hth-type transcriptional regulator cynr;
PDBTitle: structure of the ligand binding domain of e. coli cynr, a2 transcriptional regulator controlling cyanate metabolism
92c3ho7A_



not modelled 97.3 13 PDB header:transcription
Chain: A: PDB Molecule:oxyr;
PDBTitle: crystal structure of oxyr from porphyromonas gingivalis
93c3kn3C_



not modelled 97.0 12 PDB header:transcription
Chain: C: PDB Molecule:putative periplasmic protein;
PDBTitle: crystal structure of lysr substrate binding domain (25-263) of2 putative periplasmic protein from wolinella succinogenes
94c3r6uA_



not modelled 97.0 12 PDB header:transport protein
Chain: A: PDB Molecule:choline-binding protein;
PDBTitle: crystal structure of choline binding protein opubc from bacillus2 subtilis
95c3lr1A_



not modelled 97.0 13 PDB header:transport protein
Chain: A: PDB Molecule:tungstate abc transporter, periplasmic tungstate-
PDBTitle: the crystal structure of the tungstate abc transporter from2 geobacter sulfurreducens
96c2hzkB_



not modelled 97.0 11 PDB header:ligand binding, transport protein
Chain: B: PDB Molecule:trap-t family sorbitol/mannitol transporter, periplasmic
PDBTitle: crystal structures of a sodium-alpha-keto acid binding subunit from a2 trap transporter in its open form
97d2ozza1



not modelled 96.9 15 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
98d2nxoa1



not modelled 96.8 16 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
99c1xsfA_



not modelled 96.7 22 PDB header:cell cycle, hydrolase
Chain: A: PDB Molecule:probable resuscitation-promoting factor rpfb;
PDBTitle: solution structure of a resuscitation promoting factor2 domain from mycobacterium tuberculosis
100d1ixca2



not modelled 96.6 14 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
101c1al3A_



not modelled 96.6 16 PDB header:transcription regulation
Chain: A: PDB Molecule:cys regulon transcriptional activator cysb;
PDBTitle: cofactor binding fragment of cysb from klebsiella aerogenes
102d1al3a_



not modelled 96.6 16 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
103c3jv9B_



not modelled 96.6 12 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator, lysr family;
PDBTitle: the structure of a reduced form of oxyr from n. meningitidis
104d1i6aa_



not modelled 96.5 14 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
105d1utha_



not modelled 96.5 9 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
106d1xsfa1



not modelled 96.5 22 Fold:Lysozyme-like
Superfamily:Lysozyme-like
Family:RPF-like
107c3eq1A_



not modelled 96.4 13 PDB header:transferase
Chain: A: PDB Molecule:porphobilinogen deaminase;
PDBTitle: the crystal structure of human porphobilinogen deaminase at2 2.8a resolution
108d1r9la_



not modelled 95.8 16 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
109c2uyeA_



not modelled 95.7 9 PDB header:transcription
Chain: A: PDB Molecule:regulatory protein;
PDBTitle: double mutant y110s,f111v dntr from burkholderia sp. strain2 dnt in complex with thiocyanate
110c3oxnD_



not modelled 95.6 10 PDB header:transcription regulator
Chain: D: PDB Molecule:putative transcriptional regulator, lysr family;
PDBTitle: the crystal structure of a putative transcriptional regulator from2 vibrio parahaemolyticus
111d1b1xa1



not modelled 95.5 11 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Transferrin
112d1eh3a_



not modelled 95.4 12 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Transferrin
113c3fj7A_



not modelled 95.4 12 PDB header:protein binding
Chain: A: PDB Molecule:major antigenic peptide peb3;
PDBTitle: crystal structure of l-phospholactate bound peb3
114c2vd3B_



not modelled 95.4 17 PDB header:transferase
Chain: B: PDB Molecule:atp phosphoribosyltransferase;
PDBTitle: the structure of histidine inhibited hisg from2 methanobacterium thermoautotrophicum
115d1dtza1



not modelled 95.3 10 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Transferrin
116d1sw5a_



not modelled 95.2 10 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
117c3eo5A_



not modelled 94.9 22 PDB header:cell adhesion
Chain: A: PDB Molecule:resuscitation-promoting factor rpfb;
PDBTitle: crystal structure of the resuscitation promoting factor rpfb
118c1twyG_



not modelled 94.7 11 PDB header:structural genomics, unknown function
Chain: G: PDB Molecule:abc transporter, periplasmic substrate-binding protein;
PDBTitle: crystal structure of an abc-type phosphate transport receptor from2 vibrio cholerae
119d1twya_



not modelled 94.7 11 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
120c3pppA_



not modelled 94.7 13 PDB header:transport protein
Chain: A: PDB Molecule:glycine betaine/carnitine/choline-binding protein;
PDBTitle: structures of the substrate-binding protein provide insights into the2 multiple compatible solutes binding specificities of bacillus3 subtilis abc transporter opuc

Binding site prediction 

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite



Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
 
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
 
© Structural Bioinformatics Group
Imperial College London
Lawrence Kelley, Benjamin Jefferys
Disclaimer
Terms and Conditions
Component software
Template detection: HHpred 1.51
Secondary structure prediction: Psi-pred 2.5
Disorder prediction: Disopred 2.4
Transmembrane prediction: Memsat_SVM
Multi-template modelling and ab initio: Poing 1.0