Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP27249
DateThu Jan 5 11:43:29 GMT 2012
Unique Job ID2ff26d4812459fb6

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1v4aA_
Top template information
PDB header:transferase
Chain: A: PDB Molecule:glutamate-ammonia-ligase adenylyltransferase;
PDBTitle: structure of the n-terminal domain of escherichia coli2 glutamine synthetase adenylyltransferase
Confidence and coverage
Confidence:100.0% Coverage: 34%
300 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.
803 residues ( 90%) 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  MNTLPEQYANTALPTLPGQPQNPCVWPRDELTVGGIKAHIDTFQRWLGDAFDNGISAEQL
Secondary structure 
SS confidence 
Disorder  ????????
????????????????????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  IEARTEFIDQLLQRLWIEAGFSQIADLALVAVGGYGRGELHPLSDVDLLILSRKKLPDDQ
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  AQKVGELLTLLWDVKLEVGHSVRTLEECMLEGLSDLTVATNLIESRLLIGDVALFLELQK
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  HIFSEGFWPSDKFYAAKVEEQNQRHQRYHGTSYNLEPDIKSSPGGLRDIHTLQWVARRHF
Secondary structure 
SS confidence 
Disorder 
???????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  GATSLDEMVGFGFLTSAERAELNECLHILWRIRFALHLVVSRYDNRLLFDRQLSVAQRLN
Secondary structure 
SS confidence 
Disorder 
???
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  YSGEGNEPVERMMKDYFRVTRRVSELNQMLLQLFDEAILALPADEKPRPIDDEFQLRGTL
Secondary structure 
SS confidence 
Disorder 
?????
????????
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  IDLRDETLFMRQPEAILRMFYTMVHNSAITGIYSTTLRQLRHARRHLQQPLCNIPEARKL
Secondary structure 
SS confidence 
Disorder 
?
???
?
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  FLSILRHPGAVRRGLLPMHRHSVLGAYMPQWSHIVGQMQFDLFHAYTVDEHTIRVMLKLE
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  SFASEETRQRHPLCVDVWPRLPSTELIFIAALFHDIAKGRGGDHSILGAQDVVHFAELHG
Secondary structure 
SS confidence 
Disorder 
????
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  LNSRETQLVAWLVRQHLLMSVTAQRRDIQDPEVIKQFAEEVQTENRLRYLVCLTVADICA
Secondary structure 
SS confidence 
Disorder 
????
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  TNETLWNSWKQSLLRELYFATEKQLRRGMQNTPDMRERVRHHQLQALALLRMDNIDEEAL
Secondary structure 
SS confidence 
Disorder 
?????????
??????
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  HQIWSRCRANYFVRHSPNQLAWHARHLLQHDLSKPLVLLSPQATRGGTEIFIWSPDRPYL
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........730.........740.........750.........760.........770.........780
Sequence  FAAVCAELDRRNLSVHDAQIFTTRDGMAMDTFIVLEPDGNPLSADRHEVIRFGLEQVLTQ
Secondary structure 
SS confidence 
Disorder 
?????
Disorder confidence 
 
   .........790.........800.........810.........820.........830.........840
Sequence  SSWQPPQPRRQPAKLRHFTVETEVTFLPTHTDRKSFLELIALDQPGLLARVGKIFADLGI
Secondary structure 
SS confidence 
Disorder  ????????????????????
Disorder confidence 
 
   .........850.........860.........870.........880.........890
Sequence  SLHGARITTIGERVEDLFIIATADRRALNNELQQEVHQRLTEALNPNDKG
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 1v4a chain A

3D model

Region: 27 - 331
Aligned: 300
Modelled: 305
Confidence: 100.0%
Identity: 15%
PDB header:transferase
Chain: A: PDB Molecule:glutamate-ammonia-ligase adenylyltransferase;
PDBTitle: structure of the n-terminal domain of escherichia coli2 glutamine synthetase adenylyltransferase

Phyre2

PDB 3k7d chain A

3D model

Region: 4 - 299
Aligned: 296
Modelled: 296
Confidence: 100.0%
Identity: 17%
PDB header:transferase
Chain: A: PDB Molecule:glutamate-ammonia-ligase adenylyltransferase;
PDBTitle: c-terminal (adenylylation) domain of e.coli glutamine synthetase2 adenylyltransferase

Phyre2

PDB 3aqn chain A

3D model

Region: 356 - 611
Aligned: 237
Modelled: 256
Confidence: 100.0%
Identity: 12%
PDB header:transferase
Chain: A: PDB Molecule:poly(a) polymerase;
PDBTitle: complex structure of bacterial protein (apo form ii)

Phyre2

PDB 1v4a chain A domain 2

3D model

Region: 4 - 189
Aligned: 186
Modelled: 186
Confidence: 100.0%
Identity: 14%
Fold: Nucleotidyltransferase
Superfamily: Nucleotidyltransferase
Family: GlnE-like domain

Phyre2

PDB 1v4a chain A domain 1

3D model

Region: 190 - 331
Aligned: 136
Modelled: 142
Confidence: 99.9%
Identity: 18%
Fold: Four-helical up-and-down bundle
Superfamily: Nucleotidyltransferase substrate binding subunit/domain
Family: Glutamine synthase adenylyltransferase GlnE, domain 2

Phyre2

PDB 1u8s chain B

3D model

Region: 705 - 888
Aligned: 159
Modelled: 171
Confidence: 99.8%
Identity: 14%
PDB header:transcription
Chain: B: PDB Molecule:glycine cleavage system transcriptional
PDBTitle: crystal structure of putative glycine cleavage system2 transcriptional repressor

Phyre2

PDB 2nyi chain B

3D model

Region: 704 - 882
Aligned: 153
Modelled: 162
Confidence: 99.8%
Identity: 18%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:unknown protein;
PDBTitle: crystal structure of an unknown protein from galdieria2 sulphuraria

Phyre2

PDB 1miy chain B

3D model

Region: 356 - 611
Aligned: 197
Modelled: 223
Confidence: 99.7%
Identity: 16%
PDB header:translation, transferase
Chain: B: PDB Molecule:trna cca-adding enzyme;
PDBTitle: crystal structure of bacillus stearothermophilus cca-adding enzyme in2 complex with ctp

Phyre2

PDB 1vfg chain B

3D model

Region: 356 - 561
Aligned: 170
Modelled: 184
Confidence: 99.7%
Identity: 16%
PDB header:transferase/rna
Chain: B: PDB Molecule:poly a polymerase;
PDBTitle: crystal structure of trna nucleotidyltransferase complexed2 with a primer trna and an incoming atp analog

Phyre2

PDB 1vfg chain A domain 1

3D model

Region: 360 - 610
Aligned: 210
Modelled: 229
Confidence: 99.7%
Identity: 15%
Fold: Poly A polymerase C-terminal region-like
Superfamily: Poly A polymerase C-terminal region-like
Family: Poly A polymerase C-terminal region-like

Phyre2

PDB 1miw chain A domain 1

3D model

Region: 368 - 613
Aligned: 187
Modelled: 209
Confidence: 99.6%
Identity: 15%
Fold: Poly A polymerase C-terminal region-like
Superfamily: Poly A polymerase C-terminal region-like
Family: Poly A polymerase C-terminal region-like

Phyre2

PDB 3h37 chain B

3D model

Region: 356 - 567
Aligned: 174
Modelled: 188
Confidence: 99.5%
Identity: 14%
PDB header:transferase
Chain: B: PDB Molecule:trna nucleotidyl transferase-related protein;
PDBTitle: the structure of cca-adding enzyme apo form i

Phyre2

PDB 1ou5 chain A

3D model

Region: 356 - 556
Aligned: 152
Modelled: 166
Confidence: 99.5%
Identity: 13%
PDB header:translation, transferase
Chain: A: PDB Molecule:trna cca-adding enzyme;
PDBTitle: crystal structure of human cca-adding enzyme

Phyre2

PDB 1ou5 chain A domain 1

3D model

Region: 365 - 555
Aligned: 140
Modelled: 156
Confidence: 99.3%
Identity: 13%
Fold: Poly A polymerase C-terminal region-like
Superfamily: Poly A polymerase C-terminal region-like
Family: Poly A polymerase C-terminal region-like

Phyre2

PDB 2pq7 chain A domain 1

3D model

Region: 444 - 601
Aligned: 135
Modelled: 142
Confidence: 98.9%
Identity: 25%
Fold: HD-domain/PDEase-like
Superfamily: HD-domain/PDEase-like
Family: HD domain

Phyre2

PDB 2qgs chain A domain 1

3D model

Region: 459 - 556
Aligned: 81
Modelled: 97
Confidence: 98.7%
Identity: 22%
Fold: HD-domain/PDEase-like
Superfamily: HD-domain/PDEase-like
Family: HD domain

Phyre2

PDB 3djb chain A domain 1

3D model

Region: 459 - 590
Aligned: 95
Modelled: 99
Confidence: 98.6%
Identity: 26%
Fold: HD-domain/PDEase-like
Superfamily: HD-domain/PDEase-like
Family: HD domain

Phyre2

PDB 2f06 chain B

3D model

Region: 709 - 888
Aligned: 133
Modelled: 150
Confidence: 98.5%
Identity: 18%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:conserved hypothetical protein;
PDBTitle: crystal structure of protein bt0572 from bacteroides thetaiotaomicron

Phyre2

PDB 3ibw chain A

3D model

Region: 811 - 881
Aligned: 66
Modelled: 64
Confidence: 98.3%
Identity: 11%
PDB header:transferase
Chain: A: PDB Molecule:gtp pyrophosphokinase;
PDBTitle: crystal structure of the act domain from gtp2 pyrophosphokinase of chlorobium tepidum. northeast3 structural genomics consortium target ctr148a

Phyre2

PDB 1kny chain A domain 2

3D model

Region: 62 - 181
Aligned: 113
Modelled: 120
Confidence: 98.2%
Identity: 14%
Fold: Nucleotidyltransferase
Superfamily: Nucleotidyltransferase
Family: Kanamycin nucleotidyltransferase (KNTase), N-terminal domain

Phyre2

PDB 3ccg chain A

3D model

Region: 469 - 645
Aligned: 134
Modelled: 131
Confidence: 97.8%
Identity: 22%
PDB header:hydrolase
Chain: A: PDB Molecule:hd superfamily hydrolase;
PDBTitle: crystal structure of predicted hd superfamily hydrolase involved in2 nad metabolism (np_347894.1) from clostridium acetobutylicum at 1.503 a resolution

Phyre2

PDB 3l76 chain B

3D model

Region: 655 - 844
Aligned: 143
Modelled: 143
Confidence: 96.9%
Identity: 20%
PDB header:transferase
Chain: B: PDB Molecule:aspartokinase;
PDBTitle: crystal structure of aspartate kinase from synechocystis

Phyre2
1
c1v4aA_
2
c3k7dA_
3
c3aqnA_
4
d1v4aa2
5
d1v4aa1
6
c1u8sB_
7
c2nyiB_
8
c1miyB_
9
c1vfgB_
10
d1vfga1
11
d1miwa1
12
c3h37B_
13
c1ou5A_
14
d1ou5a1
15
d2pq7a1
16
d2qgsa1
17
d3djba1
18
c2f06B_
19
c3ibwA_
20
d1knya2
21
22
23
24
25
26
27
28
29
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31
c3ccgA_
32
33
34
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c3l76B_
51
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1v4aA_
100.0 15 PDB header:transferase
Chain: A: PDB Molecule:glutamate-ammonia-ligase adenylyltransferase;
PDBTitle: structure of the n-terminal domain of escherichia coli2 glutamine synthetase adenylyltransferase
2c3k7dA_
100.0 17 PDB header:transferase
Chain: A: PDB Molecule:glutamate-ammonia-ligase adenylyltransferase;
PDBTitle: c-terminal (adenylylation) domain of e.coli glutamine synthetase2 adenylyltransferase
3c3aqnA_
100.0 12 PDB header:transferase
Chain: A: PDB Molecule:poly(a) polymerase;
PDBTitle: complex structure of bacterial protein (apo form ii)
4d1v4aa2
100.0 14 Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:GlnE-like domain
5d1v4aa1
99.9 18 Fold:Four-helical up-and-down bundle
Superfamily:Nucleotidyltransferase substrate binding subunit/domain
Family:Glutamine synthase adenylyltransferase GlnE, domain 2
6c1u8sB_
99.8 14 PDB header:transcription
Chain: B: PDB Molecule:glycine cleavage system transcriptional
PDBTitle: crystal structure of putative glycine cleavage system2 transcriptional repressor
7c2nyiB_
99.8 18 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:unknown protein;
PDBTitle: crystal structure of an unknown protein from galdieria2 sulphuraria
8c1miyB_
99.7 16 PDB header:translation, transferase
Chain: B: PDB Molecule:trna cca-adding enzyme;
PDBTitle: crystal structure of bacillus stearothermophilus cca-adding enzyme in2 complex with ctp
9c1vfgB_
99.7 16 PDB header:transferase/rna
Chain: B: PDB Molecule:poly a polymerase;
PDBTitle: crystal structure of trna nucleotidyltransferase complexed2 with a primer trna and an incoming atp analog
10d1vfga1
99.7 15 Fold:Poly A polymerase C-terminal region-like
Superfamily:Poly A polymerase C-terminal region-like
Family:Poly A polymerase C-terminal region-like
11d1miwa1
99.6 15 Fold:Poly A polymerase C-terminal region-like
Superfamily:Poly A polymerase C-terminal region-like
Family:Poly A polymerase C-terminal region-like
12c3h37B_
99.5 14 PDB header:transferase
Chain: B: PDB Molecule:trna nucleotidyl transferase-related protein;
PDBTitle: the structure of cca-adding enzyme apo form i
13c1ou5A_
99.5 13 PDB header:translation, transferase
Chain: A: PDB Molecule:trna cca-adding enzyme;
PDBTitle: crystal structure of human cca-adding enzyme
14d1ou5a1
99.3 13 Fold:Poly A polymerase C-terminal region-like
Superfamily:Poly A polymerase C-terminal region-like
Family:Poly A polymerase C-terminal region-like
15d2pq7a1
98.9 25 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:HD domain
16d2qgsa1
98.7 22 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:HD domain
17d3djba1
98.6 26 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:HD domain
18c2f06B_
98.5 18 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:conserved hypothetical protein;
PDBTitle: crystal structure of protein bt0572 from bacteroides thetaiotaomicron
19c3ibwA_
98.3 11 PDB header:transferase
Chain: A: PDB Molecule:gtp pyrophosphokinase;
PDBTitle: crystal structure of the act domain from gtp2 pyrophosphokinase of chlorobium tepidum. northeast3 structural genomics consortium target ctr148a
20d1knya2
98.2 14 Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:Kanamycin nucleotidyltransferase (KNTase), N-terminal domain
21d1u8sa2
not modelled 98.1 15 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:Glycine cleavage system transcriptional repressor
22d3dtoa1
not modelled 98.1 29 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:HD domain
23d3b57a1
not modelled 98.0 21 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:HD domain
24d1zpva1
not modelled 98.0 18 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:SP0238-like
25d1u8sa1
not modelled 98.0 18 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:Glycine cleavage system transcriptional repressor
26c3gw7A_
not modelled 97.9 20 PDB header:hydrolase
Chain: A: PDB Molecule:uncharacterized protein yedj;
PDBTitle: crystal structure of a metal-dependent phosphohydrolase2 with conserved hd domain (yedj) from escherichia coli in3 complex with nickel ions. northeast structural genomics4 consortium target er63
27c3p96A_
not modelled 97.9 12 PDB header:hydrolase
Chain: A: PDB Molecule:phosphoserine phosphatase serb;
PDBTitle: crystal structure of phosphoserine phosphatase serb from mycobacterium2 avium, native form
28c3m5fA_
not modelled 97.9 20 PDB header:hydrolase
Chain: A: PDB Molecule:metal dependent phosphohydrolase;
PDBTitle: structure of mj0384, a cas3 protein from methanocaldococcus jannaschii
29c2q14A_
not modelled 97.9 18 PDB header:hydrolase
Chain: A: PDB Molecule:phosphohydrolase;
PDBTitle: crystal structure of phosphohydrolase (bt4208) from bacteroides2 thetaiotaomicron vpi-5482 at 2.20 a resolution
30c2o08B_
not modelled 97.9 26 PDB header:hydrolase
Chain: B: PDB Molecule:bh1327 protein;
PDBTitle: crystal structure of a putative hd superfamily hydrolase (bh1327) from2 bacillus halodurans at 1.90 a resolution
31c3ccgA_
97.8 22 PDB header:hydrolase
Chain: A: PDB Molecule:hd superfamily hydrolase;
PDBTitle: crystal structure of predicted hd superfamily hydrolase involved in2 nad metabolism (np_347894.1) from clostridium acetobutylicum at 1.503 a resolution
32c3skdA_
not modelled 97.8 15 PDB header:hydrolase
Chain: A: PDB Molecule:putative uncharacterized protein tthb187;
PDBTitle: crystal structure of the thermus thermophilus cas3 hd domain in the2 presence of ni2+
33c2ogiA_
not modelled 97.6 25 PDB header:hydrolase
Chain: A: PDB Molecule:hypothetical protein sag1661;
PDBTitle: crystal structure of a putative metal dependent phosphohydrolase2 (sag1661) from streptococcus agalactiae serogroup v at 1.85 a3 resolution
34d2pjqa1
not modelled 97.5 18 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:HD domain
35d1u6za1
not modelled 97.5 25 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:Ppx associated domain
36c3n0vD_
not modelled 97.5 8 PDB header:hydrolase
Chain: D: PDB Molecule:formyltetrahydrofolate deformylase;
PDBTitle: crystal structure of a formyltetrahydrofolate deformylase (pp_0327)2 from pseudomonas putida kt2440 at 2.25 a resolution
37c3o1lB_
not modelled 97.5 15 PDB header:hydrolase
Chain: B: PDB Molecule:formyltetrahydrofolate deformylase;
PDBTitle: crystal structure of a formyltetrahydrofolate deformylase (pspto_4314)2 from pseudomonas syringae pv. tomato str. dc3000 at 2.20 a resolution
38d2o6ia1
not modelled 97.4 15 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:HD domain
39c2o6iA_
not modelled 97.4 15 PDB header:hydrolase
Chain: A: PDB Molecule:hd domain protein;
PDBTitle: structure of an enterococcus faecalis hd domain phosphohydrolase
40d1ygya3
not modelled 97.4 19 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
41c3obiC_
not modelled 97.3 15 PDB header:hydrolase
Chain: C: PDB Molecule:formyltetrahydrofolate deformylase;
PDBTitle: crystal structure of a formyltetrahydrofolate deformylase (np_949368)2 from rhodopseudomonas palustris cga009 at 1.95 a resolution
42c2dqbB_
not modelled 97.3 20 PDB header:hydrolase, dna binding protein
Chain: B: PDB Molecule:deoxyguanosinetriphosphate triphosphohydrolase, putative;
PDBTitle: crystal structure of dntp triphosphohydrolase from thermus2 thermophilus hb8, which is homologous to dgtp triphosphohydrolase
43c3nrbD_
not modelled 97.2 17 PDB header:hydrolase
Chain: D: PDB Molecule:formyltetrahydrofolate deformylase;
PDBTitle: crystal structure of a formyltetrahydrofolate deformylase (puru,2 pp_1943) from pseudomonas putida kt2440 at 2.05 a resolution
44d2heka1
not modelled 97.2 16 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:HD domain
45c1knyA_
not modelled 97.2 19 PDB header:transferase
Chain: A: PDB Molecule:kanamycin nucleotidyltransferase;
PDBTitle: kanamycin nucleotidyltransferase
46c2rffA_
not modelled 97.1 18 PDB header:transferase
Chain: A: PDB Molecule:putative nucleotidyltransferase;
PDBTitle: crystal structure of a putative nucleotidyltransferase2 (np_343093.1) from sulfolobus solfataricus at 1.40 a3 resolution
47c3hc1A_
not modelled 97.0 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized hdod domain protein;
PDBTitle: crystal structure of hdod domain protein with unknown function2 (np_953345.1) from geobacter sulfurreducens at 1.90 a resolution
48d1sc6a3
not modelled 97.0 14 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
49d2f1fa1
not modelled 96.9 14 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:IlvH-like
50c3l76B_
96.9 20 PDB header:transferase
Chain: B: PDB Molecule:aspartokinase;
PDBTitle: crystal structure of aspartate kinase from synechocystis
51c2floA_
not modelled 96.9 20 PDB header:hydrolase
Chain: A: PDB Molecule:exopolyphosphatase;
PDBTitle: crystal structure of exopolyphosphatase (ppx) from e. coli o157:h7
52d2pc6a2
not modelled 96.8 15 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:IlvH-like
53d2gz4a1
not modelled 96.8 18 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:HD domain
54c3m1tA_
not modelled 96.8 15 PDB header:hydrolase
Chain: A: PDB Molecule:putative phosphohydrolase;
PDBTitle: crystal structure of putative phosphohydrolase (yp_929327.1) from2 shewanella amazonensis sb2b at 1.62 a resolution
55c3louB_
not modelled 96.8 16 PDB header:hydrolase
Chain: B: PDB Molecule:formyltetrahydrofolate deformylase;
PDBTitle: crystal structure of formyltetrahydrofolate deformylase (yp_105254.1)2 from burkholderia mallei atcc 23344 at 1.90 a resolution
56c3hi0B_
not modelled 96.7 11 PDB header:hydrolase
Chain: B: PDB Molecule:putative exopolyphosphatase;
PDBTitle: crystal structure of putative exopolyphosphatase (17739545) from2 agrobacterium tumefaciens str. c58 (dupont) at 2.30 a resolution
57c3memA_
not modelled 96.7 17 PDB header:signaling protein
Chain: A: PDB Molecule:putative signal transduction protein;
PDBTitle: crystal structure of a putative signal transduction protein2 (maqu_0641) from marinobacter aquaeolei vt8 at 2.25 a resolution
58d2f06a1
not modelled 96.7 13 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:BT0572-like
59c1ygyA_
not modelled 96.7 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:d-3-phosphoglycerate dehydrogenase;
PDBTitle: crystal structure of d-3-phosphoglycerate dehydrogenase from2 mycobacterium tuberculosis
60c3u1nC_
not modelled 96.6 20 PDB header:hydrolase
Chain: C: PDB Molecule:sam domain and hd domain-containing protein 1;
PDBTitle: structure of the catalytic core of human samhd1
61d1vqra_
not modelled 96.6 13 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:modified HD domain
62d1no5a_
not modelled 96.6 21 Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:Catalytic subunit of bi-partite nucleotidyltransferase
63c2f1fA_
not modelled 96.4 14 PDB header:transferase
Chain: A: PDB Molecule:acetolactate synthase isozyme iii small subunit;
PDBTitle: crystal structure of the regulatory subunit of2 acetohydroxyacid synthase isozyme iii from e. coli
64d1ylqa1
not modelled 96.4 19 Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:Catalytic subunit of bi-partite nucleotidyltransferase
65d1taza_
not modelled 96.2 18 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:PDEase
66c2pc6C_
not modelled 96.1 15 PDB header:lyase
Chain: C: PDB Molecule:probable acetolactate synthase isozyme iii (small subunit);
PDBTitle: crystal structure of putative acetolactate synthase- small subunit2 from nitrosomonas europaea
67d2fgca2
not modelled 96.1 12 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:IlvH-like
68c3ljvA_
not modelled 95.8 10 PDB header:transcription
Chain: A: PDB Molecule:mmoq response regulator;
PDBTitle: crystal structure of mmoq response regulator (fragment 29-302) from2 methylococcus capsulatus str. bath, northeast structural genomics3 consortium target mcr175m
69c2fgcA_
not modelled 95.8 12 PDB header:transferase
Chain: A: PDB Molecule:acetolactate synthase, small subunit;
PDBTitle: crystal structure of acetolactate synthase- small subunit from2 thermotoga maritima
70d2f06a2
not modelled 95.8 20 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:BT0572-like
71c3i7aA_
not modelled 95.7 7 PDB header:hydrolase
Chain: A: PDB Molecule:putative metal-dependent phosphohydrolase;
PDBTitle: crystal structure of putative metal-dependent phosphohydrolase2 (yp_926882.1) from shewanella amazonensis sb2b at 2.06 a resolution
72c2pgsA_
not modelled 95.7 18 PDB header:hydrolase
Chain: A: PDB Molecule:putative deoxyguanosinetriphosphate triphosphohydrolase;
PDBTitle: crystal structure of a putative deoxyguanosinetriphosphate2 triphosphohydrolase from pseudomonas syringae pv. phaseolicola 1448a
73c1zklA_
not modelled 95.6 17 PDB header:hydrolase
Chain: A: PDB Molecule:high-affinity camp-specific 3',5'-cyclic
PDBTitle: multiple determinants for inhibitor selectivity of cyclic2 nucleotide phosphodiesterases
74d1wota_
not modelled 95.5 26 Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:Catalytic subunit of bi-partite nucleotidyltransferase
75d1so2a_
not modelled 95.5 19 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:PDEase
76d1f0ja_
not modelled 95.4 20 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:PDEase
77c3g3nA_
not modelled 95.2 17 PDB header:hydrolase
Chain: A: PDB Molecule:high affinity camp-specific 3',5'-cyclic
PDBTitle: pde7a catalytic domain in complex with 3-(2,6-2 difluorophenyl)-2-(methylthio)quinazolin-4(3h)-one
78c2zhoB_
not modelled 95.1 19 PDB header:transferase
Chain: B: PDB Molecule:aspartokinase;
PDBTitle: crystal structure of the regulatory subunit of aspartate2 kinase from thermus thermophilus (ligand free form)
79c3qi4A_
not modelled 94.8 15 PDB header:hydrolase
Chain: A: PDB Molecule:high affinity cgmp-specific 3',5'-cyclic phosphodiesterase
PDBTitle: crystal structure of pde9a(q453e) in complex with ibmx
80c2dtjA_
not modelled 94.8 17 PDB header:transferase
Chain: A: PDB Molecule:aspartokinase;
PDBTitle: crystal structure of regulatory subunit of aspartate kinase2 from corynebacterium glutamicum
81c3kq5A_
not modelled 94.4 16 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical cytosolic protein;
PDBTitle: crystal structure of an uncharacterized protein from coxiella burnetii
82d1phza1
not modelled 93.7 14 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:Phenylalanine metabolism regulatory domain
83c3c66B_
not modelled 93.7 18 PDB header:transferase
Chain: B: PDB Molecule:poly(a) polymerase;
PDBTitle: yeast poly(a) polymerase in complex with fip1 residues 80-105
84c1xotB_
not modelled 93.3 19 PDB header:hydrolase
Chain: B: PDB Molecule:camp-specific 3',5'-cyclic phosphodiesterase 4b;
PDBTitle: catalytic domain of human phosphodiesterase 4b in complex with2 vardenafil
85d2qmwa2
not modelled 93.1 25 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:Phenylalanine metabolism regulatory domain
86c2r8qA_
not modelled 93.0 15 PDB header:hydrolase
Chain: A: PDB Molecule:class i phosphodiesterase pdeb1;
PDBTitle: structure of lmjpdeb1 in complex with ibmx
87c3luyA_
not modelled 92.8 17 PDB header:isomerase
Chain: A: PDB Molecule:probable chorismate mutase;
PDBTitle: putative chorismate mutase from bifidobacterium adolescentis
88c3mwbA_
not modelled 92.8 19 PDB header:lyase
Chain: A: PDB Molecule:prephenate dehydratase;
PDBTitle: the crystal structure of prephenate dehydratase in complex with l-phe2 from arthrobacter aurescens to 2.0a
89c3bg2A_
not modelled 92.8 23 PDB header:hydrolase
Chain: A: PDB Molecule:dgtp triphosphohydrolase;
PDBTitle: crystal structure of deoxyguanosinetriphosphate triphosphohydrolase2 from flavobacterium sp. med217
90c3mtjA_
not modelled 92.7 22 PDB header:oxidoreductase
Chain: A: PDB Molecule:homoserine dehydrogenase;
PDBTitle: the crystal structure of a homoserine dehydrogenase from thiobacillus2 denitrificans to 2.15a
91d1q79a2
not modelled 92.4 11 Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:Poly(A) polymerase, PAP, N-terminal domain
92c2qmxB_
not modelled 92.3 15 PDB header:ligase
Chain: B: PDB Molecule:prephenate dehydratase;
PDBTitle: the crystal structure of l-phe inhibited prephenate dehydratase from2 chlorobium tepidum tls
93c2ounA_
not modelled 92.2 19 PDB header:hydrolase
Chain: A: PDB Molecule:camp and camp-inhibited cgmp 3',5'-cyclic
PDBTitle: crystal structure of pde10a2 in complex with amp
94d1jmsa4
not modelled 92.1 24 Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:DNA polymerase beta-like
95c1q78A_
not modelled 92.0 11 PDB header:transferase
Chain: A: PDB Molecule:poly(a) polymerase alpha;
PDBTitle: crystal structure of poly(a) polymerase in complex with 3'-2 datp and magnesium chloride
96c1xozA_
not modelled 91.9 16 PDB header:hydrolase
Chain: A: PDB Molecule:cgmp-specific 3',5'-cyclic phosphodiesterase;
PDBTitle: catalytic domain of human phosphodiesterase 5a in complex2 with tadalafil
97c3ibjB_
not modelled 91.8 14 PDB header:hydrolase
Chain: B: PDB Molecule:cgmp-dependent 3',5'-cyclic phosphodiesterase;
PDBTitle: x-ray structure of pde2a
98d1y2ka1
not modelled 91.5 15 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:PDEase
99d1tbfa_
not modelled 91.1 15 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:PDEase
100d2q66a2
not modelled 91.1 21 Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:Poly(A) polymerase, PAP, N-terminal domain
101c1z1lA_
not modelled 90.6 14 PDB header:hydrolase
Chain: A: PDB Molecule:cgmp-dependent 3',5'-cyclic phosphodiesterase;
PDBTitle: the crystal structure of the phosphodiesterase 2a catalytic2 domain
102d3dy8a1
not modelled 90.5 15 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:PDEase
103c1kdhA_
not modelled 90.3 16 PDB header:transferase/dna
Chain: A: PDB Molecule:terminal deoxynucleotidyltransferase short
PDBTitle: binary complex of murine terminal deoxynucleotidyl2 transferase with a primer single stranded dna
104c2re1A_
not modelled 90.0 19 PDB header:transferase
Chain: A: PDB Molecule:aspartokinase, alpha and beta subunits;
PDBTitle: crystal structure of aspartokinase alpha and beta subunits
105c3mzoA_
not modelled 89.7 20 PDB header:hydrolase
Chain: A: PDB Molecule:lin2634 protein;
PDBTitle: crystal structure of a hd-domain phosphohydrolase (lin2634) from2 listeria innocua at 1.98 a resolution
106c3nqwB_
not modelled 88.6 19 PDB header:hydrolase
Chain: B: PDB Molecule:cg11900;
PDBTitle: a metazoan ortholog of spot hydrolyzes ppgpp and plays a role in2 starvation responses
107c2o8hA_
not modelled 88.3 18 PDB header:hydrolase
Chain: A: PDB Molecule:phosphodiesterase-10a;
PDBTitle: crystal structure of the catalytic domain of rat2 phosphodiesterase 10a
108c2cqzA_
not modelled 88.2 18 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:177aa long hypothetical protein;
PDBTitle: crystal structure of ph0347 protein from pyrococcus horikoshii ot3
109d2h44a1
not modelled 87.4 15 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:PDEase
110c3jz0B_
not modelled 87.2 23 PDB header:transferase/antibiotic
Chain: B: PDB Molecule:lincosamide nucleotidyltransferase;
PDBTitle: linb complexed with clindamycin and ampcpp
111c3bjcA_
not modelled 87.0 15 PDB header:hydrolase
Chain: A: PDB Molecule:cgmp-specific 3',5'-cyclic phosphodiesterase;
PDBTitle: crystal structure of the pde5a catalytic domain in complex2 with a novel inhibitor
112c2huoA_
not modelled 85.6 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:inositol oxygenase;
PDBTitle: crystal structure of mouse myo-inositol oxygenase in complex with2 substrate
113d3bxda1
not modelled 85.6 20 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:MioX-like
114d2hmfa3
not modelled 85.1 14 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:Aspartokinase allosteric domain-like
115d1ynba1
not modelled 84.6 24 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:HD domain
116c1sz1A_
not modelled 83.2 19 PDB header:transferase/rna
Chain: A: PDB Molecule:trna nucleotidyltransferase;
PDBTitle: mechanism of cca-adding enzymes specificity revealed by crystal2 structures of ternary complexes
117d2ibna1
not modelled 83.0 23 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:MioX-like
118d2paqa1
not modelled 81.8 24 Fold:HD-domain/PDEase-like
Superfamily:HD-domain/PDEase-like
Family:HD domain
119c2qmwA_
not modelled 81.6 23 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:prephenate dehydratase;
PDBTitle: the crystal structure of the prephenate dehydratase (pdt) from2 staphylococcus aureus subsp. aureus mu50
120d2fmpa3
not modelled 80.6 13 Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:DNA polymerase beta-like

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