Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP22525
DateThu Jan 5 11:38:56 GMT 2012
Unique Job IDb49ab12f3f68dcc3

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2hklB_
Top template information
PDB header:transferase
Chain: B: PDB Molecule:l,d-transpeptidase;
PDBTitle: crystal structure of enterococcus faecium l,d-2 transpeptidase c442s mutant
Confidence and coverage
Confidence: 99.6% Coverage: 18%
112 residues ( 18% of your sequence) have been modelled with 99.6% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
200 residues ( 33%) 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  MLLNMMCGRQLSAISLCLAVTFAPLFNAQADEPEVIPGDSPVAVSEQGEALPQAQATAIM
Secondary structure 
SS confidence 
Disorder  ????
???
???????????????????????????????????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  AGIQPLPEGAAEKARTQIESQLPAGYKPVYLNQLQLLYAARDMQPMWENRDAVKAFQQQL
Secondary structure 
SS confidence 
Disorder  ?????????????
??????????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  AEVAIAGFQPQFNKWVELLTDPGVNGMARDVVLSDAMMGYLHFIANIPVKGTRWLYSSKP
Secondary structure 
SS confidence 
Disorder 
?
??
?
???
?
???
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  YALATPPLSVINQWQLALDKGQLPTFVAGLAPQHPQYAAMHESLLALLCDTKPWPQLTGK
Secondary structure 
SS confidence 
Disorder  ???
?????
?
????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  ATLRPGQWSNDVPALREILQRTGMLDGGPKITLPGDDTPTDAVVSPSAVTVETAETKPMD
Secondary structure 
SS confidence 
Disorder  ?
?
?
?
????????????????????????????????
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  KQTTSRSKPAPAVRAAYDNELVEAVKRFQAWQGLGADGAIGPATRDWLNVTPAQRAGVLA
Secondary structure 
SS confidence 
Disorder 
????????????
????
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  LNIQRLRLLPTELSTGIMVNIPAYSLVYYQNGNQVLDSRVIVGRPDRKTPMMSSALNNVV
Secondary structure 
SS confidence 
Disorder  ??
?
?
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  VNPPWNVPPTLARKDILPKVRNDPGYLESHGYTVMRGWNSREAIDPWQVDWSTITASNLP
Secondary structure 
SS confidence 
Disorder 
?
???
?
??
????
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  FRFQQAPGPRNSLGRYKFNMPSSEAIYLHDTPNHNLFKRDTRALSSGCVRVNKASDLANM
Secondary structure 
SS confidence 
Disorder 
?
?
?
???
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  LLQDAGWNDKRISDALKQGDTRYVNIRQSIPVNLYYLTAFVGADGRTQYRTDIYNYDLPA
Secondary structure 
SS confidence 
Disorder 
?
??
Disorder confidence 
 
   .........610.....
Sequence  RSSSQIVSKAEQLIR
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 2hkl chain B

3D model

Region: 370 - 541
Aligned: 112
Modelled: 114
Confidence: 99.6%
Identity: 21%
PDB header:transferase
Chain: B: PDB Molecule:l,d-transpeptidase;
PDBTitle: crystal structure of enterococcus faecium l,d-2 transpeptidase c442s mutant

Phyre2

PDB 1zat chain A domain 1

3D model

Region: 372 - 541
Aligned: 112
Modelled: 113
Confidence: 99.5%
Identity: 24%
Fold: L,D-transpeptidase catalytic domain-like
Superfamily: L,D-transpeptidase catalytic domain-like
Family: L,D-transpeptidase catalytic domain-like

Phyre2

PDB 1lbu chain A domain 1

3D model

Region: 241 - 349
Aligned: 67
Modelled: 67
Confidence: 99.2%
Identity: 34%
Fold: PGBD-like
Superfamily: PGBD-like
Family: Peptidoglycan binding domain, PGBD

Phyre2

PDB 1y7m chain B

3D model

Region: 368 - 541
Aligned: 104
Modelled: 108
Confidence: 99.2%
Identity: 29%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:hypothetical protein bsu14040;
PDBTitle: crystal structure of the b. subtilis ykud protein at 2 a2 resolution

Phyre2

PDB 1lbu chain A

3D model

Region: 240 - 349
Aligned: 68
Modelled: 68
Confidence: 99.1%
Identity: 34%
PDB header:hydrolase
Chain: A: PDB Molecule:muramoyl-pentapeptide carboxypeptidase;
PDBTitle: hydrolase metallo (zn) dd-peptidase

Phyre2

PDB 3bkh chain A

3D model

Region: 241 - 368
Aligned: 84
Modelled: 83
Confidence: 99.1%
Identity: 29%
PDB header:hydrolase
Chain: A: PDB Molecule:lytic transglycosylase;
PDBTitle: crystal structure of the bacteriophage phikz lytic2 transglycosylase, gp144

Phyre2

PDB 1y7m chain A domain 1

3D model

Region: 370 - 541
Aligned: 102
Modelled: 106
Confidence: 99.1%
Identity: 30%
Fold: L,D-transpeptidase catalytic domain-like
Superfamily: L,D-transpeptidase catalytic domain-like
Family: L,D-transpeptidase catalytic domain-like

Phyre2

PDB 2bh7 chain A

3D model

Region: 241 - 348
Aligned: 62
Modelled: 62
Confidence: 98.2%
Identity: 19%
PDB header:hydrolase
Chain: A: PDB Molecule:n-acetylmuramoyl-l-alanine amidase;
PDBTitle: crystal structure of a semet derivative of amid at 2.22 angstroms

Phyre2

PDB 1l6j chain A

3D model

Region: 245 - 442
Aligned: 101
Modelled: 105
Confidence: 97.3%
Identity: 26%
PDB header:hydrolase
Chain: A: PDB Molecule:matrix metalloproteinase-9;
PDBTitle: crystal structure of human matrix metalloproteinase mmp92 (gelatinase b).

Phyre2

PDB 1eak chain A domain 1

3D model

Region: 248 - 351
Aligned: 58
Modelled: 58
Confidence: 97.1%
Identity: 16%
Fold: PGBD-like
Superfamily: PGBD-like
Family: MMP N-terminal domain

Phyre2

PDB 2ikb chain A domain 1

3D model

Region: 323 - 369
Aligned: 46
Modelled: 47
Confidence: 97.0%
Identity: 28%
Fold: Lysozyme-like
Superfamily: Lysozyme-like
Family: NMB1012-like

Phyre2

PDB 1slm chain A domain 1

3D model

Region: 318 - 351
Aligned: 34
Modelled: 34
Confidence: 97.0%
Identity: 18%
Fold: PGBD-like
Superfamily: PGBD-like
Family: MMP N-terminal domain

Phyre2

PDB 1slm chain A

3D model

Region: 318 - 351
Aligned: 34
Modelled: 34
Confidence: 97.0%
Identity: 18%
PDB header:hydrolase
Chain: A: PDB Molecule:stromelysin-1;
PDBTitle: crystal structure of fibroblast stromelysin-1: the c-truncated human2 proenzyme

Phyre2

PDB 1su3 chain A domain 1

3D model

Region: 316 - 351
Aligned: 36
Modelled: 36
Confidence: 96.8%
Identity: 22%
Fold: PGBD-like
Superfamily: PGBD-like
Family: MMP N-terminal domain

Phyre2

PDB 1su3 chain A

3D model

Region: 316 - 351
Aligned: 36
Modelled: 36
Confidence: 96.7%
Identity: 22%
PDB header:hydrolase
Chain: A: PDB Molecule:interstitial collagenase;
PDBTitle: x-ray structure of human prommp-1: new insights into2 collagenase action

Phyre2

PDB 1eak chain A

3D model

Region: 320 - 351
Aligned: 32
Modelled: 32
Confidence: 96.5%
Identity: 22%
PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:72 kda type iv collagenase;
PDBTitle: catalytic domain of prommp-2 e404q mutant

Phyre2

PDB 2nr7 chain A domain 1

3D model

Region: 324 - 365
Aligned: 42
Modelled: 42
Confidence: 96.3%
Identity: 21%
Fold: Lysozyme-like
Superfamily: Lysozyme-like
Family: NMB1012-like

Phyre2

PDB 1l6j chain A domain 1

3D model

Region: 321 - 351
Aligned: 31
Modelled: 31
Confidence: 96.2%
Identity: 23%
Fold: PGBD-like
Superfamily: PGBD-like
Family: MMP N-terminal domain

Phyre2

PDB 1gxd chain A

3D model

Region: 321 - 351
Aligned: 31
Modelled: 31
Confidence: 93.0%
Identity: 23%
PDB header:hydrolase
Chain: A: PDB Molecule:72 kda type iv collagenase;
PDBTitle: prommp-2/timp-2 complex

Phyre2

PDB 3a05 chain A

3D model

Region: 487 - 557
Aligned: 66
Modelled: 67
Confidence: 74.1%
Identity: 24%
PDB header:ligase
Chain: A: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of tryptophanyl-trna synthetase from2 hyperthermophilic archaeon, aeropyrum pernix k1 complex3 with tryptophan

Phyre2
1
c2hklB_
2
d1zata1
3
d1lbua1
4
c1y7mB_
5
c1lbuA_
6
c3bkhA_
7
d1y7ma1
8
c2bh7A_
9
c1l6jA_
10
d1eaka1
11
d2ikba1
12
d1slma1
13
c1slmA_
14
d1su3a1
15
c1su3A_
16
c1eakA_
17
d2nr7a1
18
d1l6ja1
19
c1gxdA_
20
c3a05A_
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
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2hklB_
99.6 21 PDB header:transferase
Chain: B: PDB Molecule:l,d-transpeptidase;
PDBTitle: crystal structure of enterococcus faecium l,d-2 transpeptidase c442s mutant
2d1zata1
99.5 24 Fold:L,D-transpeptidase catalytic domain-like
Superfamily:L,D-transpeptidase catalytic domain-like
Family:L,D-transpeptidase catalytic domain-like
3d1lbua1
99.2 34 Fold:PGBD-like
Superfamily:PGBD-like
Family:Peptidoglycan binding domain, PGBD
4c1y7mB_
99.2 29 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:hypothetical protein bsu14040;
PDBTitle: crystal structure of the b. subtilis ykud protein at 2 a2 resolution
5c1lbuA_
99.1 34 PDB header:hydrolase
Chain: A: PDB Molecule:muramoyl-pentapeptide carboxypeptidase;
PDBTitle: hydrolase metallo (zn) dd-peptidase
6c3bkhA_
99.1 29 PDB header:hydrolase
Chain: A: PDB Molecule:lytic transglycosylase;
PDBTitle: crystal structure of the bacteriophage phikz lytic2 transglycosylase, gp144
7d1y7ma1
99.1 30 Fold:L,D-transpeptidase catalytic domain-like
Superfamily:L,D-transpeptidase catalytic domain-like
Family:L,D-transpeptidase catalytic domain-like
8c2bh7A_
98.2 19 PDB header:hydrolase
Chain: A: PDB Molecule:n-acetylmuramoyl-l-alanine amidase;
PDBTitle: crystal structure of a semet derivative of amid at 2.22 angstroms
9c1l6jA_
97.3 26 PDB header:hydrolase
Chain: A: PDB Molecule:matrix metalloproteinase-9;
PDBTitle: crystal structure of human matrix metalloproteinase mmp92 (gelatinase b).
10d1eaka1
97.1 16 Fold:PGBD-like
Superfamily:PGBD-like
Family:MMP N-terminal domain
11d2ikba1
97.0 28 Fold:Lysozyme-like
Superfamily:Lysozyme-like
Family:NMB1012-like
12d1slma1
97.0 18 Fold:PGBD-like
Superfamily:PGBD-like
Family:MMP N-terminal domain
13c1slmA_
97.0 18 PDB header:hydrolase
Chain: A: PDB Molecule:stromelysin-1;
PDBTitle: crystal structure of fibroblast stromelysin-1: the c-truncated human2 proenzyme
14d1su3a1
96.8 22 Fold:PGBD-like
Superfamily:PGBD-like
Family:MMP N-terminal domain
15c1su3A_
96.7 22 PDB header:hydrolase
Chain: A: PDB Molecule:interstitial collagenase;
PDBTitle: x-ray structure of human prommp-1: new insights into2 collagenase action
16c1eakA_
96.5 22 PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:72 kda type iv collagenase;
PDBTitle: catalytic domain of prommp-2 e404q mutant
17d2nr7a1
96.3 21 Fold:Lysozyme-like
Superfamily:Lysozyme-like
Family:NMB1012-like
18d1l6ja1
96.2 23 Fold:PGBD-like
Superfamily:PGBD-like
Family:MMP N-terminal domain
19c1gxdA_
93.0 23 PDB header:hydrolase
Chain: A: PDB Molecule:72 kda type iv collagenase;
PDBTitle: prommp-2/timp-2 complex
20c3a05A_
74.1 24 PDB header:ligase
Chain: A: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of tryptophanyl-trna synthetase from2 hyperthermophilic archaeon, aeropyrum pernix k1 complex3 with tryptophan
21d2bgxa1
not modelled 67.0 20 Fold:PGBD-like
Superfamily:PGBD-like
Family:Peptidoglycan binding domain, PGBD
22d2oo3a1
not modelled 49.4 27 Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:LPG1296-like
23c2rjbD_
not modelled 45.2 23 PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of uncharacterized protein ydcj (sf1787)2 from shigella flexneri which includes domain duf1338.3 northeast structural genomics consortium target sfr276
24c2juoA_
not modelled 40.4 33 PDB header:transcription
Chain: A: PDB Molecule:ga-binding protein alpha chain;
PDBTitle: gabpa ost domain
25c3n9iA_
not modelled 38.2 15 PDB header:ligase
Chain: A: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of tryptophanyl-trna synthetase from yersinia pestis2 co92
26c1wsuA_
not modelled 35.6 12 PDB header:translation/rna
Chain: A: PDB Molecule:selenocysteine-specific elongation factor;
PDBTitle: c-terminal domain of elongation factor selb complexed with2 secis rna
27d2ns0a1
not modelled 34.4 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:RHA1 ro06458-like
28d1r1ga_
not modelled 30.2 67 Fold:Knottins (small inhibitors, toxins, lectins)
Superfamily:Scorpion toxin-like
Family:Short-chain scorpion toxins
29c1r1gB_
not modelled 30.2 67 PDB header:toxin
Chain: B: PDB Molecule:neurotoxin bmk37;
PDBTitle: crystal structure of the scorpion toxin bmbkttx1
30c1r1gA_
not modelled 30.2 67 PDB header:toxin
Chain: A: PDB Molecule:neurotoxin bmk37;
PDBTitle: crystal structure of the scorpion toxin bmbkttx1
31d2d69a1
not modelled 29.3 19 Fold:TIM beta/alpha-barrel
Superfamily:RuBisCo, C-terminal domain
Family:RuBisCo, large subunit, C-terminal domain
32c2d69B_
not modelled 25.9 19 PDB header:lyase
Chain: B: PDB Molecule:ribulose bisphosphate carboxylase;
PDBTitle: crystal structure of the complex of sulfate ion and octameric2 ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) from3 pyrococcus horikoshii ot3 (form-2 crystal)
33c2r5kE_
not modelled 25.8 27 PDB header:viral protein
Chain: E: PDB Molecule:major capsid protein l1;
PDBTitle: pentamer structure of major capsid protein l1 of human2 papilloma virus type 11
34c3phuA_
not modelled 24.5 28 PDB header:hydrolase
Chain: A: PDB Molecule:rna-directed rna polymerase l;
PDBTitle: otu domain of crimean congo hemorrhagic fever virus
35c2r5iL_
not modelled 23.8 24 PDB header:viral protein
Chain: L: PDB Molecule:l1 protein;
PDBTitle: pentamer structure of major capsid protein l1 of human2 papilloma virus type 18
36c3pt2A_
not modelled 23.4 30 PDB header:hydrolase/protein binding
Chain: A: PDB Molecule:rna polymerase;
PDBTitle: structure of a viral otu domain protease bound to ubiquitin
37c1dzlA_
not modelled 23.1 27 PDB header:virus
Chain: A: PDB Molecule:late major capsid protein l1;
PDBTitle: l1 protein of human papillomavirus 16
38d1dzla_
not modelled 23.1 27 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily:Group I dsDNA viruses
Family:Papovaviridae-like VP
39c3qm2A_
not modelled 22.7 20 PDB header:transferase
Chain: A: PDB Molecule:phosphoserine aminotransferase;
PDBTitle: 2.25 angstrom crystal structure of phosphoserine aminotransferase2 (serc) from salmonella enterica subsp. enterica serovar typhimurium
40c3jxeB_
not modelled 22.1 24 PDB header:ligase
Chain: B: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of pyrococcus horikoshii tryptophanyl-trna2 synthetase in complex with trpamp
41c3hv0A_
not modelled 21.6 20 PDB header:ligase
Chain: A: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: tryptophanyl-trna synthetase from cryptosporidium parvum
42c2yy5C_
not modelled 21.4 19 PDB header:ligase
Chain: C: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of tryptophanyl-trna synthetase from mycoplasma2 pneumoniae
43d1i6la_
not modelled 20.8 16 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
44c2lafA_
not modelled 20.4 14 PDB header:membrane protein
Chain: A: PDB Molecule:lipoprotein 34;
PDBTitle: nmr solution structure of the n-terminal domain of the e. coli2 lipoprotein bamc
45c2zviB_
not modelled 20.2 20 PDB header:isomerase
Chain: B: PDB Molecule:2,3-diketo-5-methylthiopentyl-1-phosphate
PDBTitle: crystal structure of 2,3-diketo-5-methylthiopentyl-1-2 phosphate enolase from bacillus subtilis
46d1ykwa1
not modelled 20.0 12 Fold:TIM beta/alpha-barrel
Superfamily:RuBisCo, C-terminal domain
Family:RuBisCo, large subunit, C-terminal domain
47d2p0la1
not modelled 19.5 20 Fold:Class II aaRS and biotin synthetases
Superfamily:Class II aaRS and biotin synthetases
Family:LplA-like
48c3iyjE_
not modelled 19.2 18 PDB header:virus
Chain: E: PDB Molecule:major capsid protein l1;
PDBTitle: bovine papillomavirus type 1 outer capsid
49d1ej7l1
not modelled 18.2 17 Fold:TIM beta/alpha-barrel
Superfamily:RuBisCo, C-terminal domain
Family:RuBisCo, large subunit, C-terminal domain
50c2qygC_
not modelled 17.8 16 PDB header:unknown function
Chain: C: PDB Molecule:ribulose bisphosphate carboxylase-like protein 2;
PDBTitle: crystal structure of a rubisco-like protein rlp2 from rhodopseudomonas2 palustris
51c2j5bA_
not modelled 17.6 19 PDB header:ligase
Chain: A: PDB Molecule:tyrosyl-trna synthetase;
PDBTitle: structure of the tyrosyl trna synthetase from acanthamoeba2 polyphaga mimivirus complexed with tyrosynol
52c2ip1A_
not modelled 17.2 34 PDB header:ligase
Chain: A: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure analysis of s. cerevisiae tryptophanyl trna2 synthetase
53c3elyA_
not modelled 17.1 25 PDB header:transferase
Chain: A: PDB Molecule:methyltransferase;
PDBTitle: wesselsbron virus methyltransferase in complex with adohcy
54c1gehE_
not modelled 16.7 12 PDB header:lyase
Chain: E: PDB Molecule:ribulose-1,5-bisphosphate carboxylase/oxygenase;
PDBTitle: crystal structure of archaeal rubisco (ribulose 1,5-bisphosphate2 carboxylase/oxygenase)
55d3ci0j1
not modelled 16.5 19 Fold:Pili subunits
Superfamily:Pili subunits
Family:EpsJ-like
56c2xvsA_
not modelled 16.4 21 PDB header:antitumor protein
Chain: A: PDB Molecule:tetratricopeptide repeat protein 5;
PDBTitle: crystal structure of human ttc5 (strap) c-terminal ob2 domain
57c1telA_
not modelled 16.4 12 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:ribulose bisphosphate carboxylase, large subunit;
PDBTitle: crystal structure of a rubisco-like protein from chlorobium2 tepidum
58c2oxtC_
not modelled 16.2 28 PDB header:viral protein
Chain: C: PDB Molecule:nucleoside-2'-o-methyltransferase;
PDBTitle: crystal structure of meaban virus nucleoside-2'-o-2 methyltransferase
59d1geha1
not modelled 16.1 12 Fold:TIM beta/alpha-barrel
Superfamily:RuBisCo, C-terminal domain
Family:RuBisCo, large subunit, C-terminal domain
60d1wuua1
not modelled 16.0 26 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:GHMP Kinase, N-terminal domain
61c2plyB_
not modelled 15.8 12 PDB header:translation/rna
Chain: B: PDB Molecule:selenocysteine-specific elongation factor;
PDBTitle: structure of the mrna binding fragment of elongation factor2 selb in complex with secis rna.
62d1rbla1
not modelled 15.8 17 Fold:TIM beta/alpha-barrel
Superfamily:RuBisCo, C-terminal domain
Family:RuBisCo, large subunit, C-terminal domain
63d1pgsa2
not modelled 15.4 26 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily:PHM/PNGase F
Family:Glycosyl-asparaginase
64d1iufa2
not modelled 14.4 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Centromere-binding
65c2i6oA_
not modelled 14.2 18 PDB header:hydrolase
Chain: A: PDB Molecule:sulfolobus solfataricus protein tyrosine
PDBTitle: crystal structure of the complex of the archaeal sulfolobus2 ptp-fold phosphatase with phosphopeptides n-g-(p)y-k-n
66d1vlra2
not modelled 13.5 24 Fold:mRNA decapping enzyme DcpS N-terminal domain
Superfamily:mRNA decapping enzyme DcpS N-terminal domain
Family:mRNA decapping enzyme DcpS N-terminal domain
67c1zswA_
not modelled 13.2 10 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:glyoxalase family protein;
PDBTitle: crystal structure of bacillus cereus metallo protein from glyoxalase2 family
68c3nwrA_
not modelled 13.2 16 PDB header:lyase
Chain: A: PDB Molecule:a rubisco-like protein;
PDBTitle: crystal structure of a rubisco-like protein from burkholderia fungorum
69c3nk4B_
not modelled 12.8 25 PDB header:cell adhesion
Chain: B: PDB Molecule:zona pellucida 3;
PDBTitle: crystal structure of full-length sperm receptor zp3 at 2.0 a2 resolution
70c2quiB_
not modelled 12.3 20 PDB header:ligase
Chain: B: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structures of human tryptophanyl-trna synthetase in2 complex with tryptophanamide and atp
71c3hzrD_
not modelled 12.1 26 PDB header:ligase
Chain: D: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: tryptophanyl-trna synthetase homolog from entamoeba histolytica
72c1r6uB_
not modelled 11.9 24 PDB header:ligase
Chain: B: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of an active fragment of human tryptophanyl-trna2 synthetase with cytokine activity
73d2p5ia1
not modelled 11.8 19 Fold:Class II aaRS and biotin synthetases
Superfamily:Class II aaRS and biotin synthetases
Family:LplA-like
74d2z15a1
not modelled 11.7 16 Fold:BTG domain-like
Superfamily:BTG domain-like
Family:BTG domain-like
75d8ruca1
not modelled 11.7 20 Fold:TIM beta/alpha-barrel
Superfamily:RuBisCo, C-terminal domain
Family:RuBisCo, large subunit, C-terminal domain
76d3bl9a2
not modelled 11.4 25 Fold:mRNA decapping enzyme DcpS N-terminal domain
Superfamily:mRNA decapping enzyme DcpS N-terminal domain
Family:mRNA decapping enzyme DcpS N-terminal domain
77c2gezE_
not modelled 11.4 11 PDB header:hydrolase
Chain: E: PDB Molecule:l-asparaginase alpha subunit;
PDBTitle: crystal structure of potassium-independent plant asparaginase
78c3sz3A_
not modelled 11.3 12 PDB header:ligase
Chain: A: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of tryptophanyl-trna synthetase from vibrio cholerae2 with an endogenous tryptophan
79d3e9va1
not modelled 11.1 23 Fold:BTG domain-like
Superfamily:BTG domain-like
Family:BTG domain-like
80c3focB_
not modelled 11.1 26 PDB header:ligase
Chain: B: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: tryptophanyl-trna synthetase from giardia lamblia
81c1rcxH_
not modelled 11.0 17 PDB header:lyase (carbon-carbon)
Chain: H: PDB Molecule:ribulose bisphosphate carboxylase/oxygenase;
PDBTitle: non-activated spinach rubisco in complex with its substrate2 ribulose-1,5-bisphosphate
82d1atga_
not modelled 10.7 15 Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
83c1vqzA_
not modelled 10.7 15 PDB header:ligase
Chain: A: PDB Molecule:lipoate-protein ligase, putative;
PDBTitle: crystal structure of a putative lipoate-protein ligase a (sp_1160)2 from streptococcus pneumoniae tigr4 at 1.99 a resolution
84d1bwva1
not modelled 10.5 25 Fold:TIM beta/alpha-barrel
Superfamily:RuBisCo, C-terminal domain
Family:RuBisCo, large subunit, C-terminal domain
85c2yfnA_
not modelled 10.4 18 PDB header:hydrolase
Chain: A: PDB Molecule:alpha-galactosidase-sucrose kinase agask;
PDBTitle: galactosidase domain of alpha-galactosidase-sucrose kinase,2 agask
86c1bqfA_
not modelled 10.0 57 PDB header:hormone/growth factor
Chain: A: PDB Molecule:protein (growth-blocking peptide);
PDBTitle: growth-blocking peptide (gbp) from pseudaletia separata
87c2kimA_
not modelled 9.7 17 PDB header:transferase
Chain: A: PDB Molecule:o6-methylguanine-dna methyltransferase;
PDBTitle: 1.7-mm microcryoprobe solution nmr structure of an o6-2 methylguanine dna methyltransferase family protein from3 vibrio parahaemolyticus. northeast structural genomics4 consortium target vpr247.
88c3qfwB_
not modelled 9.6 18 PDB header:lyase
Chain: B: PDB Molecule:ribulose-1,5-bisphosphate carboxylase/oxygenase large
PDBTitle: crystal structure of rubisco-like protein from rhodopseudomonas2 palustris
89c3prhB_
not modelled 8.5 20 PDB header:ligase
Chain: B: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: tryptophanyl-trna synthetase val144pro mutant from b. subtilis
90c1iufA_
not modelled 8.5 18 PDB header:dna binding protein
Chain: A: PDB Molecule:centromere abp1 protein;
PDBTitle: low resolution solution structure of the two dna-binding2 domains in schizosaccharomyces pombe abp1 protein
91d1vqza2
not modelled 8.4 15 Fold:Class II aaRS and biotin synthetases
Superfamily:Class II aaRS and biotin synthetases
Family:LplA-like
92d1vlya2
not modelled 8.1 11 Fold:Folate-binding domain
Superfamily:Folate-binding domain
Family:Aminomethyltransferase folate-binding domain
93c3tgoD_
not modelled 7.9 13 PDB header:membrane protein
Chain: D: PDB Molecule:lipoprotein 34;
PDBTitle: crystal structure of the e. coli bamcd complex
94c3e4wB_
not modelled 7.9 21 PDB header:oxidoreductase
Chain: B: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of a 33kda catalase-related protein from2 mycobacterium avium subsp. paratuberculosis. p2(1)2(1)2(1) crystal3 form.
95c1sghA_
not modelled 7.8 14 PDB header:structural protein
Chain: A: PDB Molecule:moesin;
PDBTitle: moesin ferm domain bound to ebp50 c-terminal peptide
96c3m5wB_
not modelled 7.8 11 PDB header:ligase
Chain: B: PDB Molecule:tryptophanyl-trna synthetase;
PDBTitle: crystal structure of tryptophanyl-trna synthetase from2 campylobacter jejuni
97d2ibaa2
not modelled 7.7 8 Fold:T-fold
Superfamily:Tetrahydrobiopterin biosynthesis enzymes-like
Family:Urate oxidase (uricase)
98d1dgsa1
not modelled 7.5 17 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:NAD+-dependent DNA ligase, domain 3
99d1r8se_
not modelled 7.3 22 Fold:alpha-alpha superhelix
Superfamily:Sec7 domain
Family:Sec7 domain

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