Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP21514
DateThu Jan 5 11:38:25 GMT 2012
Unique Job ID12b3f1607c406156

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3pjwA_
Top template information
PDB header:lyase
Chain: A: PDB Molecule:cyclic dimeric gmp binding protein;
PDBTitle: structure of pseudomonas fluorescence lapd ggdef-eal dual domain, i23
Confidence and coverage
Confidence:100.0% Coverage: 91%
328 residues ( 91% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MNSCDFRVFLQEFGTTVHLSLPGSVSEKERLLLKLLMQGMSVTEISQYRNRSAKTISHQK
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Disorder  ????
















??

















?


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   .........70.........80.........90.........100.........110.........120
Sequence  KQLFEKLGIQSDITFWRDIFFQYNPEIISATGSNSHRYINDNHYHHIVTPEAISLALENH
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Disorder 


















??????


































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   .........130.........140.........150.........160.........170.........180
Sequence  EFKPWIQPVFCAQTGVLTGCEVLVRWEHPQTGIIPPDQFIPLAESSGLIVIMTRQLMKQT
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   .........190.........200.........210.........220.........230.........240
Sequence  ADILMPVKHLLPDNFHIGINVSAGCFLAAGFEKECLNLVNKLGNDKIKLVLELTERNPIP
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?














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   .........250.........260.........270.........280.........290.........300
Sequence  VTPEARAIFDSLHQHNITFALDDFGTGYATYRYLQAFPVDFIKIDKSFVQMASVDEISGH
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???





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
















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??
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   ..
Sequence  GG
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 3pjw chain A

3D model

Region: 2 - 348
Aligned: 328
Modelled: 337
Confidence: 100.0%
Identity: 18%
PDB header:lyase
Chain: A: PDB Molecule:cyclic dimeric gmp binding protein;
PDBTitle: structure of pseudomonas fluorescence lapd ggdef-eal dual domain, i23

Phyre2

PDB 3hvb chain B

3D model

Region: 109 - 352
Aligned: 242
Modelled: 244
Confidence: 100.0%
Identity: 21%
PDB header:hydrolase
Chain: B: PDB Molecule:protein fimx;
PDBTitle: crystal structure of the dual-domain ggdef-eal module of2 fimx from pseudomonas aeruginosa

Phyre2

PDB 3gfz chain B

3D model

Region: 60 - 346
Aligned: 266
Modelled: 287
Confidence: 100.0%
Identity: 19%
PDB header:hydrolase, signaling protein
Chain: B: PDB Molecule:klebsiella pneumoniae blrp1;
PDBTitle: klebsiella pneumoniae blrp1 ph 6 manganese/cy-digmp complex

Phyre2

PDB 3hv9 chain A

3D model

Region: 101 - 352
Aligned: 250
Modelled: 252
Confidence: 100.0%
Identity: 20%
PDB header:hydrolase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx eal domain from pseudomonas aeruginosa

Phyre2

PDB 3s83 chain A

3D model

Region: 109 - 360
Aligned: 248
Modelled: 252
Confidence: 100.0%
Identity: 30%
PDB header:signaling protein
Chain: A: PDB Molecule:ggdef family protein;
PDBTitle: crystal structure of eal domain from caulobacter crescentus cb15

Phyre2

PDB 3pfm chain A

3D model

Region: 102 - 349
Aligned: 241
Modelled: 248
Confidence: 100.0%
Identity: 21%
PDB header:signaling protein
Chain: A: PDB Molecule:ggdef domain protein;
PDBTitle: crystal structure of a eal domain of ggdef domain protein from2 pseudomonas fluorescens pf

Phyre2

PDB 2w27 chain A

3D model

Region: 111 - 348
Aligned: 229
Modelled: 238
Confidence: 100.0%
Identity: 21%
PDB header:signaling protein
Chain: A: PDB Molecule:ykui protein;
PDBTitle: crystal structure of the bacillus subtilis ykui protein,2 with an eal domain, in complex with substrate c-di-gmp and3 calcium

Phyre2

PDB 2r6o chain B

3D model

Region: 108 - 359
Aligned: 237
Modelled: 239
Confidence: 100.0%
Identity: 30%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative diguanylate cyclase/phosphodiesterase (ggdef & eal
PDBTitle: crystal structure of putative diguanylate cyclase/phosphodiesterase2 from thiobacillus denitrificans

Phyre2

PDB 2bas chain A domain 1

3D model

Region: 111 - 360
Aligned: 244
Modelled: 250
Confidence: 100.0%
Identity: 18%
Fold: TIM beta/alpha-barrel
Superfamily: EAL domain-like
Family: EAL domain

Phyre2

PDB 3kzp chain A

3D model

Region: 121 - 348
Aligned: 222
Modelled: 227
Confidence: 100.0%
Identity: 20%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative diguanylate cyclase/phosphodiesterase;
PDBTitle: crystal structure of putative diguanylate cyclase/phosphodiesterase2 from listaria monocytigenes

Phyre2

PDB 1w25 chain B

3D model

Region: 2 - 91
Aligned: 90
Modelled: 90
Confidence: 99.0%
Identity: 10%
PDB header:signaling protein
Chain: B: PDB Molecule:stalked-cell differentiation controlling protein;
PDBTitle: response regulator pled in complex with c-digmp

Phyre2

PDB 3ezu chain A

3D model

Region: 2 - 89
Aligned: 85
Modelled: 88
Confidence: 98.9%
Identity: 14%
PDB header:signaling protein
Chain: A: PDB Molecule:ggdef domain protein;
PDBTitle: crystal structure of multidomain protein of unknown function with2 ggdef-domain (np_951600.1) from geobacter sulfurreducens at 1.95 a3 resolution

Phyre2

PDB 3bre chain A

3D model

Region: 2 - 101
Aligned: 90
Modelled: 100
Confidence: 98.5%
Identity: 16%
PDB header:signaling protein
Chain: A: PDB Molecule:probable two-component response regulator;
PDBTitle: crystal structure of p.aeruginosa pa3702

Phyre2

PDB 3i5a chain A

3D model

Region: 2 - 88
Aligned: 87
Modelled: 87
Confidence: 98.4%
Identity: 14%
PDB header:signaling protein
Chain: A: PDB Molecule:response regulator/ggdef domain protein;
PDBTitle: crystal structure of full-length wpsr from pseudomonas syringae

Phyre2

PDB 3mtk chain A

3D model

Region: 2 - 105
Aligned: 88
Modelled: 104
Confidence: 97.9%
Identity: 13%
PDB header:transferase
Chain: A: PDB Molecule:diguanylate cyclase/phosphodiesterase;
PDBTitle: x-ray structure of diguanylate cyclase/phosphodiesterase from2 caldicellulosiruptor saccharolyticus, northeast structural genomics3 consortium target clr27c

Phyre2

PDB 3icl chain A

3D model

Region: 2 - 101
Aligned: 90
Modelled: 100
Confidence: 97.9%
Identity: 13%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:eal/ggdef domain protein;
PDBTitle: x-ray structure of protein (eal/ggdef domain protein) from2 m.capsulatus, northeast structural genomics consortium3 target mcr174c

Phyre2

PDB 3hvw chain A

3D model

Region: 2 - 84
Aligned: 83
Modelled: 83
Confidence: 97.8%
Identity: 7%
PDB header:lyase
Chain: A: PDB Molecule:diguanylate-cyclase (dgc);
PDBTitle: crystal structure of the ggdef domain of the pa2567 protein2 from pseudomonas aeruginosa, northeast structural genomics3 consortium target par365c

Phyre2

PDB 3hva chain A

3D model

Region: 2 - 86
Aligned: 85
Modelled: 85
Confidence: 97.8%
Identity: 11%
PDB header:transferase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa

Phyre2

PDB 3ign chain A

3D model

Region: 2 - 87
Aligned: 86
Modelled: 86
Confidence: 97.8%
Identity: 10%
PDB header:transferase
Chain: A: PDB Molecule:diguanylate cyclase;
PDBTitle: crystal structure of the ggdef domain from marinobacter2 aquaeolei diguanylate cyclase complexed with c-di-gmp -3 northeast structural genomics consortium target mqr89a

Phyre2

PDB 3i5c chain A

3D model

Region: 2 - 99
Aligned: 88
Modelled: 98
Confidence: 97.7%
Identity: 16%
PDB header:signaling protein
Chain: A: PDB Molecule:fusion of general control protein gcn4 and wspr response
PDBTitle: crystal structure of a fusion protein containing the leucine zipper of2 gcn4 and the ggdef domain of wspr from pseudomonas aeruginosa

Phyre2
1

c3pjwA_
2

c3hvbB_
3

c3gfzB_
4

c3hv9A_
5

c3s83A_
6

c3pfmA_
7

c2w27A_
8

c2r6oB_
9

d2basa1
10

c3kzpA_
11

c1w25B_
12

c3ezuA_
13

c3breA_
14

c3i5aA_
15

c3mtkA_
16

c3iclA_
17

c3hvwA_
18

c3hvaA_
19

c3ignA_
20

c3i5cA_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3pjwA_



100.0 18 PDB header:lyase
Chain: A: PDB Molecule:cyclic dimeric gmp binding protein;
PDBTitle: structure of pseudomonas fluorescence lapd ggdef-eal dual domain, i23
2c3hvbB_



100.0 21 PDB header:hydrolase
Chain: B: PDB Molecule:protein fimx;
PDBTitle: crystal structure of the dual-domain ggdef-eal module of2 fimx from pseudomonas aeruginosa
3c3gfzB_



100.0 19 PDB header:hydrolase, signaling protein
Chain: B: PDB Molecule:klebsiella pneumoniae blrp1;
PDBTitle: klebsiella pneumoniae blrp1 ph 6 manganese/cy-digmp complex
4c3hv9A_



100.0 20 PDB header:hydrolase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx eal domain from pseudomonas aeruginosa
5c3s83A_



100.0 30 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef family protein;
PDBTitle: crystal structure of eal domain from caulobacter crescentus cb15
6c3pfmA_



100.0 21 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef domain protein;
PDBTitle: crystal structure of a eal domain of ggdef domain protein from2 pseudomonas fluorescens pf
7c2w27A_



100.0 21 PDB header:signaling protein
Chain: A: PDB Molecule:ykui protein;
PDBTitle: crystal structure of the bacillus subtilis ykui protein,2 with an eal domain, in complex with substrate c-di-gmp and3 calcium
8c2r6oB_



100.0 30 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative diguanylate cyclase/phosphodiesterase (ggdef & eal
PDBTitle: crystal structure of putative diguanylate cyclase/phosphodiesterase2 from thiobacillus denitrificans
9d2basa1



100.0 18 Fold:TIM beta/alpha-barrel
Superfamily:EAL domain-like
Family:EAL domain
10c3kzpA_



100.0 20 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative diguanylate cyclase/phosphodiesterase;
PDBTitle: crystal structure of putative diguanylate cyclase/phosphodiesterase2 from listaria monocytigenes
11c1w25B_



99.0 10 PDB header:signaling protein
Chain: B: PDB Molecule:stalked-cell differentiation controlling protein;
PDBTitle: response regulator pled in complex with c-digmp
12c3ezuA_



98.9 14 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef domain protein;
PDBTitle: crystal structure of multidomain protein of unknown function with2 ggdef-domain (np_951600.1) from geobacter sulfurreducens at 1.95 a3 resolution
13c3breA_



98.5 16 PDB header:signaling protein
Chain: A: PDB Molecule:probable two-component response regulator;
PDBTitle: crystal structure of p.aeruginosa pa3702
14c3i5aA_



98.4 14 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator/ggdef domain protein;
PDBTitle: crystal structure of full-length wpsr from pseudomonas syringae
15c3mtkA_



97.9 13 PDB header:transferase
Chain: A: PDB Molecule:diguanylate cyclase/phosphodiesterase;
PDBTitle: x-ray structure of diguanylate cyclase/phosphodiesterase from2 caldicellulosiruptor saccharolyticus, northeast structural genomics3 consortium target clr27c
16c3iclA_



97.9 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:eal/ggdef domain protein;
PDBTitle: x-ray structure of protein (eal/ggdef domain protein) from2 m.capsulatus, northeast structural genomics consortium3 target mcr174c
17c3hvwA_



97.8 7 PDB header:lyase
Chain: A: PDB Molecule:diguanylate-cyclase (dgc);
PDBTitle: crystal structure of the ggdef domain of the pa2567 protein2 from pseudomonas aeruginosa, northeast structural genomics3 consortium target par365c
18c3hvaA_



97.8 11 PDB header:transferase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa
19c3ignA_



97.8 10 PDB header:transferase
Chain: A: PDB Molecule:diguanylate cyclase;
PDBTitle: crystal structure of the ggdef domain from marinobacter2 aquaeolei diguanylate cyclase complexed with c-di-gmp -3 northeast structural genomics consortium target mqr89a
20c3i5cA_



97.7 16 PDB header:signaling protein
Chain: A: PDB Molecule:fusion of general control protein gcn4 and wspr response
PDBTitle: crystal structure of a fusion protein containing the leucine zipper of2 gcn4 and the ggdef domain of wspr from pseudomonas aeruginosa
21d1w25a3



not modelled 97.7 12 Fold:Ferredoxin-like
Superfamily:Nucleotide cyclase
Family:GGDEF domain
22c3i5bA_



not modelled 97.6 16 PDB header:signaling protein
Chain: A: PDB Molecule:wspr response regulator;
PDBTitle: crystal structure of the isolated ggdef domain of wpsr from2 pseudomonas aeruginosa
23c3qyyB_



not modelled 97.6 19 PDB header:signaling protein/inhibitor
Chain: B: PDB Molecule:response regulator;
PDBTitle: a novel interaction mode between a microbial ggdef domain and the bis-2 (3, 5 )-cyclic di-gmp
24d1y0ea_



not modelled 96.1 9 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:NanE-like
25c3khtA_



not modelled 96.0 16 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: crystal structure of response regulator from hahella chejuensis
26c2ayxA_



not modelled 95.8 15 PDB header:transferase
Chain: A: PDB Molecule:sensor kinase protein rcsc;
PDBTitle: solution structure of the e.coli rcsc c-terminus (residues2 700-949) containing linker region and phosphoreceiver3 domain
27d1mvoa_



not modelled 95.0 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
28d1w25a1



not modelled 94.6 9 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
29d1p6qa_



not modelled 94.5 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
30c2zayA_



not modelled 94.4 12 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator receiver protein;
PDBTitle: crystal structure of response regulator from desulfuromonas2 acetoxidans
31c3nhzA_



not modelled 94.4 14 PDB header:dna binding protein
Chain: A: PDB Molecule:two component system transcriptional regulator mtra;
PDBTitle: structure of n-terminal domain of mtra
32c3hebB_



not modelled 94.0 17 PDB header:transcription regulator
Chain: B: PDB Molecule:response regulator receiver domain protein (chey);
PDBTitle: crystal structure of response regulator receiver domain from2 rhodospirillum rubrum
33c3q58A_



not modelled 94.0 15 PDB header:isomerase
Chain: A: PDB Molecule:n-acetylmannosamine-6-phosphate 2-epimerase;
PDBTitle: structure of n-acetylmannosamine-6-phosphate epimerase from salmonella2 enterica
34d2pl1a1



not modelled 93.9 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
35c3eulB_



not modelled 93.7 9 PDB header:transcription
Chain: B: PDB Molecule:possible nitrate/nitrite response transcriptional
PDBTitle: structure of the signal receiver domain of the putative2 response regulator narl from mycobacterium tuberculosis
36c2yxbA_



not modelled 93.4 12 PDB header:isomerase
Chain: A: PDB Molecule:coenzyme b12-dependent mutase;
PDBTitle: crystal structure of the methylmalonyl-coa mutase alpha-subunit from2 aeropyrum pernix
37d1heya_



not modelled 93.2 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
38d1jbea_



not modelled 93.0 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
39c3gt7A_



not modelled 92.7 11 PDB header:hydrolase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of signal receiver domain of signal2 transduction histidine kinase from syntrophus3 aciditrophicus
40c3gr7A_



not modelled 92.5 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:nadph dehydrogenase;
PDBTitle: structure of oye from geobacillus kaustophilus, hexagonal2 crystal form
41d1krwa_



not modelled 92.3 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
42c2p0oA_



not modelled 92.0 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein duf871;
PDBTitle: crystal structure of a conserved protein from locus ef_2437 in2 enterococcus faecalis with an unknown function
43d1ys7a2



not modelled 92.0 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
44d1zesa1



not modelled 91.7 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
45d1qkka_



not modelled 91.5 16 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
46d2a9pa1



not modelled 91.5 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
47d1dz3a_



not modelled 91.3 9 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
48d1k66a_



not modelled 91.3 8 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
49c3b2nA_



not modelled 91.1 10 PDB header:transcription
Chain: A: PDB Molecule:uncharacterized protein q99uf4;
PDBTitle: crystal structure of dna-binding response regulator, luxr family, from2 staphylococcus aureus
50c2jk1A_



not modelled 91.0 12 PDB header:dna-binding
Chain: A: PDB Molecule:hydrogenase transcriptional regulatory protein hupr1;
PDBTitle: crystal structure of the wild-type hupr receiver domain
51d1ua7a2



not modelled 90.8 11 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
52d1a53a_



not modelled 90.7 13 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
53d1i3ca_



not modelled 90.7 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
54c3igsB_



not modelled 90.6 16 PDB header:isomerase
Chain: B: PDB Molecule:n-acetylmannosamine-6-phosphate 2-epimerase 2;
PDBTitle: structure of the salmonella enterica n-acetylmannosamine-6-phosphate2 2-epimerase
55c2c3zA_



not modelled 90.5 13 PDB header:lyase
Chain: A: PDB Molecule:indole-3-glycerol phosphate synthase;
PDBTitle: crystal structure of a truncated variant of indole-3-2 glycerol phosphate synthase from sulfolobus solfataricus
56c3edeB_



not modelled 90.3 19 PDB header:hydrolase
Chain: B: PDB Molecule:cyclomaltodextrinase;
PDBTitle: structural base for cyclodextrin hydrolysis
57c1cygA_



not modelled 90.3 15 PDB header:glycosyltransferase
Chain: A: PDB Molecule:cyclodextrin glucanotransferase;
PDBTitle: cyclodextrin glucanotransferase (e.c.2.4.1.19) (cgtase)
58d1ny5a1



not modelled 90.3 16 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
59c3i42A_



not modelled 90.1 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:response regulator receiver domain protein (chey-
PDBTitle: structure of response regulator receiver domain (chey-like)2 from methylobacillus flagellatus
60d1zh2a1



not modelled 90.1 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
61d1yioa2



not modelled 89.9 6 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
62d1kgsa2



not modelled 89.4 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
63c3czkA_



not modelled 89.2 14 PDB header:hydrolase
Chain: A: PDB Molecule:sucrose hydrolase;
PDBTitle: crystal structure analysis of sucrose hydrolase(suh) e322q-2 sucrose complex
64d1kkoa1



not modelled 88.9 12 Fold:TIM beta/alpha-barrel
Superfamily:Enolase C-terminal domain-like
Family:D-glucarate dehydratase-like
65d1xhfa1



not modelled 88.4 8 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
66c2gjlA_



not modelled 88.4 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:hypothetical protein pa1024;
PDBTitle: crystal structure of 2-nitropropane dioxygenase
67d1u0sy_



not modelled 88.3 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
68d1a04a2



not modelled 87.9 12 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
69c2iswB_



not modelled 87.9 16 PDB header:lyase
Chain: B: PDB Molecule:putative fructose-1,6-bisphosphate aldolase;
PDBTitle: structure of giardia fructose-1,6-biphosphate aldolase in2 complex with phosphoglycolohydroxamate
70d2bhua3



not modelled 87.8 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
71d2ayxa1



not modelled 87.4 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
72d1g5aa2



not modelled 87.3 9 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
73c2rjnA_



not modelled 87.3 9 PDB header:hydrolase
Chain: A: PDB Molecule:response regulator receiver:metal-dependent
PDBTitle: crystal structure of an uncharacterized protein q2bku2 from2 neptuniibacter caesariensis
74c2zwmA_



not modelled 86.8 10 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein yycf;
PDBTitle: crystal structure of yycf receiver domain from bacillus2 subtilis
75c3cnbC_



not modelled 86.8 12 PDB header:dna binding protein
Chain: C: PDB Molecule:dna-binding response regulator, merr family;
PDBTitle: crystal structure of signal receiver domain of dna binding response2 regulator protein (merr) from colwellia psychrerythraea 34h
76d1eh9a3



not modelled 86.7 16 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
77c3cg4A_



not modelled 86.6 11 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:response regulator receiver domain protein (chey-like);
PDBTitle: crystal structure of response regulator receiver domain protein (chey-2 like) from methanospirillum hungatei jf-1
78c3lteH_



not modelled 86.5 13 PDB header:transcription
Chain: H: PDB Molecule:response regulator;
PDBTitle: crystal structure of response regulator (signal receiver domain) from2 bermanella marisrubri
79d1xm3a_



not modelled 86.4 15 Fold:TIM beta/alpha-barrel
Superfamily:ThiG-like
Family:ThiG-like
80c3t6kB_



not modelled 86.0 10 PDB header:signaling protein
Chain: B: PDB Molecule:response regulator receiver;
PDBTitle: crystal structure of a hypothetical response regulator (caur_3799)2 from chloroflexus aurantiacus j-10-fl at 1.86 a resolution
81c1tcmB_



not modelled 85.8 14 PDB header:glycosyltransferase
Chain: B: PDB Molecule:cyclodextrin glycosyltransferase;
PDBTitle: cyclodextrin glycosyltransferase w616a mutant from bacillus2 circulans strain 251
82c1qhoA_



not modelled 85.7 22 PDB header:hydrolase
Chain: A: PDB Molecule:alpha-amylase;
PDBTitle: five-domain alpha-amylase from bacillus stearothermophilus,2 maltose/acarbose complex
83c3nhmA_



not modelled 85.6 11 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: crystal structure of a response regulator from myxococcus xanthus
84c2j48A_



not modelled 85.5 11 PDB header:transferase
Chain: A: PDB Molecule:two-component sensor kinase;
PDBTitle: nmr structure of the pseudo-receiver domain of the cika2 protein.
85c3ffsC_



not modelled 85.3 14 PDB header:oxidoreductase
Chain: C: PDB Molecule:inosine-5-monophosphate dehydrogenase;
PDBTitle: the crystal structure of cryptosporidium parvum inosine-5'-2 monophosphate dehydrogenase
86d1fmfa_



not modelled 85.2 13 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
87c3bw2A_



not modelled 85.2 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:2-nitropropane dioxygenase;
PDBTitle: crystal structures and site-directed mutagenesis study of nitroalkane2 oxidase from streptomyces ansochromogenes
88d2guya2



not modelled 85.1 10 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
89c2yw3E_



not modelled 85.1 16 PDB header:lyase
Chain: E: PDB Molecule:4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-
PDBTitle: crystal structure analysis of the 4-hydroxy-2-oxoglutarate aldolase/2-2 deydro-3-deoxyphosphogluconate aldolase from tthb1
90c2qr3A_



not modelled 85.1 13 PDB header:transcription
Chain: A: PDB Molecule:two-component system response regulator;
PDBTitle: crystal structure of the n-terminal signal receiver domain of two-2 component system response regulator from bacteroides fragilis
91c2htmB_



not modelled 85.0 12 PDB header:biosynthetic protein
Chain: B: PDB Molecule:thiazole biosynthesis protein thig;
PDBTitle: crystal structure of ttha0676 from thermus thermophilus hb8
92c1bagA_



not modelled 84.8 10 PDB header:alpha-amylase
Chain: A: PDB Molecule:alpha-1,4-glucan-4-glucanohydrolase;
PDBTitle: alpha-amylase from bacillus subtilis complexed with2 maltopentaose
93c1zjaB_



not modelled 84.8 12 PDB header:isomerase
Chain: B: PDB Molecule:trehalulose synthase;
PDBTitle: crystal structure of the trehalulose synthase mutb from2 pseudomonas mesoacidophila mx-45 (triclinic form)
94d1rd5a_



not modelled 84.5 9 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
95c3hv2B_



not modelled 84.4 8 PDB header:signaling protein
Chain: B: PDB Molecule:response regulator/hd domain protein;
PDBTitle: crystal structure of signal receiver domain of hd domain-2 containing protein from pseudomonas fluorescens pf-5
96d2r25b1



not modelled 84.2 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
97c3luaA_



not modelled 84.2 10 PDB header:transcription regulator
Chain: A: PDB Molecule:response regulator receiver protein;
PDBTitle: crystal structure of a signal receiver domain of two component signal2 transduction (histidine kinase) from clostridium thermocellum
98c3grcD_



not modelled 84.1 14 PDB header:transferase
Chain: D: PDB Molecule:sensor protein, kinase;
PDBTitle: crystal structure of a sensor protein from polaromonas sp.2 js666
99c2by0A_



not modelled 84.0 14 PDB header:hydrolase
Chain: A: PDB Molecule:maltooligosyltrehalose trehalohydrolase;
PDBTitle: is radiation damage dependent on the dose-rate used during2 macromolecular crystallography data collection
100c3gl9B_



not modelled 83.7 14 PDB header:signaling protein
Chain: B: PDB Molecule:response regulator;
PDBTitle: the structure of a histidine kinase-response regulator2 complex sheds light into two-component signaling and3 reveals a novel cis autophosphorylation mechanism
101c3t8yA_



not modelled 83.7 11 PDB header:hydrolase
Chain: A: PDB Molecule:chemotaxis response regulator protein-glutamate
PDBTitle: crystal structure of the response regulator domain of thermotoga2 maritima cheb
102c2pz0B_



not modelled 83.5 15 PDB header:hydrolase
Chain: B: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of glycerophosphodiester phosphodiesterase (gdpd)2 from t. tengcongensis
103d1zgza1



not modelled 83.2 16 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
104d1h3ga3



not modelled 82.8 19 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
105c3c3mA_



not modelled 82.5 9 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator receiver protein;
PDBTitle: crystal structure of the n-terminal domain of response regulator2 receiver protein from methanoculleus marisnigri jr1
106c3f6cB_



not modelled 82.5 15 PDB header:dna binding protein
Chain: B: PDB Molecule:positive transcription regulator evga;
PDBTitle: crystal structure of n-terminal domain of positive transcription2 regulator evga from escherichia coli
107c1jibA_



not modelled 82.5 18 PDB header:hydrolase
Chain: A: PDB Molecule:neopullulanase;
PDBTitle: complex of alpha-amylase ii (tva ii) from thermoactinomyces2 vulgaris r-47 with maltotetraose based on a crystal soaked3 with maltohexaose.
108c3k8kB_



not modelled 82.3 15 PDB header:membrane protein
Chain: B: PDB Molecule:alpha-amylase, susg;
PDBTitle: crystal structure of susg
109c3c97A_



not modelled 82.2 16 PDB header:signaling protein, transferase
Chain: A: PDB Molecule:signal transduction histidine kinase;
PDBTitle: crystal structure of the response regulator receiver domain2 of a signal transduction histidine kinase from aspergillus3 oryzae
110c3crnA_



not modelled 82.2 12 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator receiver domain protein, chey-like;
PDBTitle: crystal structure of response regulator receiver domain protein (chey-2 like) from methanospirillum hungatei jf-1
111c2qvgA_



not modelled 82.1 9 PDB header:transferase
Chain: A: PDB Molecule:two component response regulator;
PDBTitle: the crystal structure of a two-component response regulator2 from legionella pneumophila
112d1ccwa_



not modelled 82.0 14 Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
113c3khjE_



not modelled 82.0 18 PDB header:oxidoreductase
Chain: E: PDB Molecule:inosine-5-monophosphate dehydrogenase;
PDBTitle: c. parvum inosine monophosphate dehydrogenase bound by inhibitor c64
114c2jrlA_



not modelled 81.9 18 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: solution structure of the beryllofluoride-activated ntrc4 receiver2 domain dimer
115d1lwha2



not modelled 81.8 13 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
116d1mb3a_



not modelled 81.7 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
117d1dbwa_



not modelled 81.6 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
118c1jgiA_



not modelled 81.6 9 PDB header:transferase
Chain: A: PDB Molecule:amylosucrase;
PDBTitle: crystal structure of the active site mutant glu328gln of2 amylosucrase from neisseria polysaccharea in complex with3 the natural substrate sucrose
119c3kruC_



not modelled 81.4 15 PDB header:oxidoreductase
Chain: C: PDB Molecule:nadh:flavin oxidoreductase/nadh oxidase;
PDBTitle: crystal structure of the thermostable old yellow enzyme from2 thermoanaerobacter pseudethanolicus e39
120c3dhuC_



not modelled 81.0 11 PDB header:hydrolase
Chain: C: PDB Molecule:alpha-amylase;
PDBTitle: crystal structure of an alpha-amylase from lactobacillus2 plantarum

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