Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP05458
DateThu Jan 5 10:58:43 GMT 2012
Unique Job IDcf8b8e4f4d36bb77

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1q2lA_
Top template information
PDB header:hydrolase
Chain: A: PDB Molecule:protease iii;
PDBTitle: crystal structure of pitrilysin
Confidence and coverage
Confidence:100.0% Coverage: 97%
937 residues ( 97% 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  MPRSTWFKALLLLVALWAPLSQAETGWQPIQETIRKSDKDNRQYQAIRLDNGMVVLLVSD
Secondary structure 
SS confidence 
Disorder  ???
?????????????????????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  PQAVKSLSALVVPVGSLEDPEAYQGLAHYLEHMSLMGSKKYPQADSLAEYLKMHGGSHNA
Secondary structure 
SS confidence 
Disorder 
?????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  STAPYRTAFYLEVENDALPGAVDRLADAIAEPLLDKKYAERERNAVNAELTMARTRDGMR
Secondary structure 
SS confidence 
Disorder 
?
????
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  MAQVSAETINPAHPGSKFSGGNLETLSDKPGNPVQQALKDFHEKYYSANLMKAVIYSNKP
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  LPELAKMAADTFGRVPNKESKKPEITVPVVTDAQKGIIIHYVPALPRKVLRVEFRIDNNS
Secondary structure 
SS confidence 
Disorder 
???????
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  AKFRSKTDELITYLIGNRSPGTLSDWLQKQGLVEGISANSDPIVNGNSGVLAISASLTDK
Secondary structure 
SS confidence 
Disorder 
??
?
????
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  GLANRDQVVAAIFSYLNLLREKGIDKQYFDELANVLDIDFRYPSITRDMDYVEWLADTMI
Secondary structure 
SS confidence 
Disorder 
???????
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  RVPVEHTLDAVNIADRYDAKAVKERLAMMTPQNARIWYISPKEPHNKTAYFVDAPYQVDK
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  ISAQTFADWQKKAADIALSLPELNPYIPDDFSLIKSEKKYDHPELIVDESNLRVVYAPSR
Secondary structure 
SS confidence 
Disorder 
?
????
?????????
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  YFASEPKADVSLILRNPKAMDSARNQVMFALNDYLAGLALDQLSNQASVGGISFSTNANN
Secondary structure 
SS confidence 
Disorder  ?
???
?
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  GLMVNANGYTQRLPQLFQALLEGYFSYTATEDQLEQAKSWYNQMMDSAEKGKAFEQAIMP
Secondary structure 
SS confidence 
Disorder 
????
??
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  AQMLSQVPYFSRDERRKILPSITLKEVLAYRDALKSGARPEFMVIGNMTEAQATTLARDV
Secondary structure 
SS confidence 
Disorder 
???
??
Disorder confidence 
 
   .........730.........740.........750.........760.........770.........780
Sequence  QKQLGADGSEWCRNKDVVVDKKQSVIFEKAGNSTDSALAAVFVPTGYDEYTSSAYSSLLG
Secondary structure 
SS confidence 
Disorder 
?
?????????
?
Disorder confidence 
 
   .........790.........800.........810.........820.........830.........840
Sequence  QIVQPWFYNQLRTEEQLGYAVFAFPMSVGRQWGMGFLLQSNDKQPSFLWERYKAFFPTAE
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........850.........860.........870.........880.........890.........900
Sequence  AKLRAMKPDEFAQIQQAVITQMLQAPQTLGEEASKLSKDFDRGNMRFDSRDKIVAQIKLL
Secondary structure 
SS confidence 
Disorder 
??????
??
?
Disorder confidence 
 
   .........910.........920.........930.........940.........950.........960
Sequence  TPQKLADFFHQAVVEPQGMAILSQISGSQNGKAEYVHPEGWKVWENVSALQQTMPLMSEK
Secondary structure 
SS confidence 
Disorder 
??
?????????????
??
??
??????
Disorder confidence 
 
   ..
Sequence  NE
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 1q2l chain A

3D model

Region: 24 - 960
Aligned: 937
Modelled: 937
Confidence: 100.0%
Identity: 100%
PDB header:hydrolase
Chain: A: PDB Molecule:protease iii;
PDBTitle: crystal structure of pitrilysin

Phyre2

PDB 2jbu chain B

3D model

Region: 26 - 958
Aligned: 930
Modelled: 933
Confidence: 100.0%
Identity: 27%
PDB header:hydrolase
Chain: B: PDB Molecule:insulin-degrading enzyme;
PDBTitle: crystal structure of human insulin degrading enzyme2 complexed with co-purified peptides.

Phyre2

PDB 2wk3 chain A

3D model

Region: 26 - 958
Aligned: 930
Modelled: 931
Confidence: 100.0%
Identity: 28%
PDB header:hydrolase
Chain: A: PDB Molecule:insulin degrading enzyme;
PDBTitle: crystal structure of human insulin-degrading enzyme in2 complex with amyloid-beta (1-42)

Phyre2

PDB 2fge chain A

3D model

Region: 37 - 945
Aligned: 883
Modelled: 902
Confidence: 100.0%
Identity: 13%
PDB header:hydrolase, plant protein
Chain: A: PDB Molecule:zinc metalloprotease (insulinase family);
PDBTitle: crystal structure of presequence protease prep from2 arabidopsis thaliana

Phyre2

PDB 1hr9 chain D

3D model

Region: 43 - 461
Aligned: 410
Modelled: 419
Confidence: 100.0%
Identity: 17%
PDB header:hydrolase
Chain: D: PDB Molecule:mitochondrial processing peptidase beta subunit;
PDBTitle: yeast mitochondrial processing peptidase beta-e73q mutant2 complexed with malate dehydrogenase signal peptide

Phyre2

PDB 1sqp chain A

3D model

Region: 43 - 463
Aligned: 407
Modelled: 420
Confidence: 100.0%
Identity: 17%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ubiquinol-cytochrome-c reductase complex core protein i,
PDBTitle: crystal structure analysis of bovine bc1 with myxothiazol

Phyre2

PDB 3eoq chain B

3D model

Region: 44 - 463
Aligned: 404
Modelled: 416
Confidence: 100.0%
Identity: 16%
PDB header:hydrolase
Chain: B: PDB Molecule:putative zinc protease;
PDBTitle: the crystal structure of putative zinc protease beta-2 subunit from thermus thermophilus hb8

Phyre2

PDB 3ami chain B

3D model

Region: 39 - 464
Aligned: 416
Modelled: 426
Confidence: 100.0%
Identity: 16%
PDB header:hydrolase
Chain: B: PDB Molecule:zinc peptidase;
PDBTitle: the crystal structure of the m16b metallopeptidase subunit from2 sphingomonas sp. a1

Phyre2

PDB 1nu1 chain A

3D model

Region: 43 - 461
Aligned: 405
Modelled: 418
Confidence: 100.0%
Identity: 17%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ubiquinol-cytochrome c reductase complex core protein i,
PDBTitle: crystal structure of mitochondrial cytochrome bc1 complexed with 2-2 nonyl-4-hydroxyquinoline n-oxide (nqno)

Phyre2

PDB 3go9 chain A

3D model

Region: 25 - 477
Aligned: 433
Modelled: 453
Confidence: 100.0%
Identity: 14%
PDB header:hydrolase
Chain: A: PDB Molecule:insulinase family protease;
PDBTitle: predicted insulinase family protease from yersinia pestis

Phyre2

PDB 1hr6 chain C

3D model

Region: 41 - 464
Aligned: 411
Modelled: 415
Confidence: 100.0%
Identity: 12%
PDB header:hydrolase
Chain: C: PDB Molecule:mitochondrial processing peptidase alpha subunit;
PDBTitle: yeast mitochondrial processing peptidase

Phyre2

PDB 3hdi chain A

3D model

Region: 45 - 468
Aligned: 407
Modelled: 424
Confidence: 100.0%
Identity: 18%
PDB header:hydrolase
Chain: A: PDB Molecule:processing protease;
PDBTitle: crystal structure of bacillus halodurans metallo peptidase

Phyre2

PDB 1l0l chain B

3D model

Region: 38 - 461
Aligned: 403
Modelled: 413
Confidence: 100.0%
Identity: 11%
PDB header:oxidoreductase
Chain: B: PDB Molecule:ubiquinol-cytochrome c reductase complex core protein 2;
PDBTitle: structure of bovine mitochondrial cytochrome bc1 complex with a bound2 fungicide famoxadone

Phyre2

PDB 3cx5 chain L

3D model

Region: 45 - 463
Aligned: 397
Modelled: 415
Confidence: 100.0%
Identity: 15%
PDB header:oxidoreductase
Chain: L: PDB Molecule:cytochrome b-c1 complex subunit 1, mitochondrial;
PDBTitle: structure of complex iii with bound cytochrome c in reduced2 state and definition of a minimal core interface for3 electron transfer.

Phyre2

PDB 3gwb chain A

3D model

Region: 43 - 464
Aligned: 404
Modelled: 416
Confidence: 100.0%
Identity: 15%
PDB header:hydrolase
Chain: A: PDB Molecule:peptidase m16 inactive domain family protein;
PDBTitle: crystal structure of peptidase m16 inactive domain from pseudomonas2 fluorescens. northeast structural genomics target plr293l

Phyre2

PDB 3amj chain B

3D model

Region: 43 - 462
Aligned: 406
Modelled: 416
Confidence: 100.0%
Identity: 16%
PDB header:hydrolase
Chain: B: PDB Molecule:zinc peptidase inactive subunit;
PDBTitle: the crystal structure of the heterodimer of m16b peptidase from2 sphingomonas sp. a1

Phyre2

PDB 3d3y chain A

3D model

Region: 47 - 464
Aligned: 401
Modelled: 418
Confidence: 100.0%
Identity: 13%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a conserved protein from enterococcus faecalis2 v583

Phyre2

PDB 1q2l chain A domain 4

3D model

Region: 24 - 263
Aligned: 240
Modelled: 240
Confidence: 100.0%
Identity: 100%
Fold: LuxS/MPP-like metallohydrolase
Superfamily: LuxS/MPP-like metallohydrolase
Family: MPP-like

Phyre2

PDB 2fge chain A domain 4

3D model

Region: 37 - 261
Aligned: 216
Modelled: 225
Confidence: 100.0%
Identity: 22%
Fold: LuxS/MPP-like metallohydrolase
Superfamily: LuxS/MPP-like metallohydrolase
Family: MPP-like

Phyre2

PDB 1ppj chain A domain 1

3D model

Region: 33 - 269
Aligned: 231
Modelled: 237
Confidence: 100.0%
Identity: 22%
Fold: LuxS/MPP-like metallohydrolase
Superfamily: LuxS/MPP-like metallohydrolase
Family: MPP-like

Phyre2
1
c1q2lA_
2
c2jbuB_
3
c2wk3A_
4
c2fgeA_
5
c1hr9D_
6
c1sqpA_
7
c3eoqB_
8
c3amiB_
9
c1nu1A_
10
c3go9A_
11
c1hr6C_
12
c3hdiA_
13
c1l0lB_
14
c3cx5L_
15
c3gwbA_
16
c3amjB_
17
c3d3yA_
18
d1q2la4
19
d2fgea4
20
d1ppja1
21
22
23
24
25
26
27
28
29
30
31
32
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1q2lA_
100.0 100 PDB header:hydrolase
Chain: A: PDB Molecule:protease iii;
PDBTitle: crystal structure of pitrilysin
2c2jbuB_
100.0 27 PDB header:hydrolase
Chain: B: PDB Molecule:insulin-degrading enzyme;
PDBTitle: crystal structure of human insulin degrading enzyme2 complexed with co-purified peptides.
3c2wk3A_
100.0 28 PDB header:hydrolase
Chain: A: PDB Molecule:insulin degrading enzyme;
PDBTitle: crystal structure of human insulin-degrading enzyme in2 complex with amyloid-beta (1-42)
4c2fgeA_
100.0 13 PDB header:hydrolase, plant protein
Chain: A: PDB Molecule:zinc metalloprotease (insulinase family);
PDBTitle: crystal structure of presequence protease prep from2 arabidopsis thaliana
5c1hr9D_
100.0 17 PDB header:hydrolase
Chain: D: PDB Molecule:mitochondrial processing peptidase beta subunit;
PDBTitle: yeast mitochondrial processing peptidase beta-e73q mutant2 complexed with malate dehydrogenase signal peptide
6c1sqpA_
100.0 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:ubiquinol-cytochrome-c reductase complex core protein i,
PDBTitle: crystal structure analysis of bovine bc1 with myxothiazol
7c3eoqB_
100.0 16 PDB header:hydrolase
Chain: B: PDB Molecule:putative zinc protease;
PDBTitle: the crystal structure of putative zinc protease beta-2 subunit from thermus thermophilus hb8
8c3amiB_
100.0 16 PDB header:hydrolase
Chain: B: PDB Molecule:zinc peptidase;
PDBTitle: the crystal structure of the m16b metallopeptidase subunit from2 sphingomonas sp. a1
9c1nu1A_
100.0 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:ubiquinol-cytochrome c reductase complex core protein i,
PDBTitle: crystal structure of mitochondrial cytochrome bc1 complexed with 2-2 nonyl-4-hydroxyquinoline n-oxide (nqno)
10c3go9A_
100.0 14 PDB header:hydrolase
Chain: A: PDB Molecule:insulinase family protease;
PDBTitle: predicted insulinase family protease from yersinia pestis
11c1hr6C_
100.0 12 PDB header:hydrolase
Chain: C: PDB Molecule:mitochondrial processing peptidase alpha subunit;
PDBTitle: yeast mitochondrial processing peptidase
12c3hdiA_
100.0 18 PDB header:hydrolase
Chain: A: PDB Molecule:processing protease;
PDBTitle: crystal structure of bacillus halodurans metallo peptidase
13c1l0lB_
100.0 11 PDB header:oxidoreductase
Chain: B: PDB Molecule:ubiquinol-cytochrome c reductase complex core protein 2;
PDBTitle: structure of bovine mitochondrial cytochrome bc1 complex with a bound2 fungicide famoxadone
14c3cx5L_
100.0 15 PDB header:oxidoreductase
Chain: L: PDB Molecule:cytochrome b-c1 complex subunit 1, mitochondrial;
PDBTitle: structure of complex iii with bound cytochrome c in reduced2 state and definition of a minimal core interface for3 electron transfer.
15c3gwbA_
100.0 15 PDB header:hydrolase
Chain: A: PDB Molecule:peptidase m16 inactive domain family protein;
PDBTitle: crystal structure of peptidase m16 inactive domain from pseudomonas2 fluorescens. northeast structural genomics target plr293l
16c3amjB_
100.0 16 PDB header:hydrolase
Chain: B: PDB Molecule:zinc peptidase inactive subunit;
PDBTitle: the crystal structure of the heterodimer of m16b peptidase from2 sphingomonas sp. a1
17c3d3yA_
100.0 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a conserved protein from enterococcus faecalis2 v583
18d1q2la4
100.0 100 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
19d2fgea4
100.0 22 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
20d1ppja1
100.0 22 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
21d1hr6b1
not modelled 100.0 24 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
22d1hr6a1
not modelled 100.0 13 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
23c3cxhM_
not modelled 100.0 14 PDB header:oxidoreductase
Chain: M: PDB Molecule:cytochrome b-c1 complex subunit 2, mitochondrial;
PDBTitle: structure of yeast complex iii with isoform-2 cytochrome c2 bound and definition of a minimal core interface for3 electron transfer.
24d1bcca1
not modelled 100.0 22 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
25d1q2la2
not modelled 100.0 100 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
26d1ppjb1
not modelled 100.0 13 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
27d1bccb1
not modelled 100.0 13 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
28d3cx5a1
not modelled 100.0 15 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
29d3cx5b1
not modelled 100.0 16 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
30d1q2la3
not modelled 100.0 100 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
31d1q2la1
not modelled 100.0 100 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
32d1ppjb2
not modelled 99.8 12 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
33d1bcca2
not modelled 99.8 7 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
34d1hr6b2
not modelled 99.8 7 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
35d1hr6a2
not modelled 99.8 11 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
36d2fgea2
not modelled 99.8 9 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
37c3ivlA_
not modelled 99.8 12 PDB header:hydrolase
Chain: A: PDB Molecule:putative zinc protease;
PDBTitle: the crystal structure of the inactive peptidase domain of a putative2 zinc protease from bordetella parapertussis to 2.2a
38d1ppja2
not modelled 99.8 6 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
39d1bccb2
not modelled 99.7 12 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
40d3cx5a2
not modelled 99.7 12 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
41d2fgea3
not modelled 99.6 12 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
42d2fgea1
not modelled 99.2 10 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:MPP-like
43c3ffvA_
not modelled 52.1 13 PDB header:protein binding
Chain: A: PDB Molecule:protein syd;
PDBTitle: crystal structure analysis of syd
44d1j96a_
not modelled 37.5 31 Fold:TIM beta/alpha-barrel
Superfamily:NAD(P)-linked oxidoreductase
Family:Aldo-keto reductases (NADP)
45d2rdea1
not modelled 22.0 18 Fold:Split barrel-like
Superfamily:PilZ domain-like
Family:PilZ domain
46c2rd9C_
not modelled 20.5 14 PDB header:hydrolase
Chain: C: PDB Molecule:bh0186 protein;
PDBTitle: crystal structure of a putative yfit-like metal-dependent hydrolase2 (bh0186) from bacillus halodurans c-125 at 2.30 a resolution
47c3hrmA_
not modelled 18.2 26 PDB header:transcription regulator
Chain: A: PDB Molecule:hth-type transcriptional regulator sarz;
PDBTitle: crystal structure of staphylococcus aureus protein sarz in sulfenic2 acid form
48d1jgsa_
not modelled 17.7 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
49d1lb3a_
not modelled 13.8 16 Fold:Ferritin-like
Superfamily:Ferritin-like
Family:Ferritin
50c3ostA_
not modelled 12.9 10 PDB header:lipid binding protein
Chain: A: PDB Molecule:serine/threonine-protein kinase kcc4;
PDBTitle: structure of the kinase associated-1 (ka1) from kcc4p
51c2kfvA_
not modelled 12.9 25 PDB header:isomerase
Chain: A: PDB Molecule:fk506-binding protein 3;
PDBTitle: structure of the amino-terminal domain of human fk506-2 binding protein 3 / northeast structural genomics3 consortium target ht99a
52c2zkr9_
not modelled 12.1 21 PDB header:ribosomal protein/rna
Chain: 9: PDB Molecule:60s ribosomal protein l32;
PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map
53d1r03a_
not modelled 11.9 18 Fold:Ferritin-like
Superfamily:Ferritin-like
Family:Ferritin
54d1xl7a1
not modelled 10.9 15 Fold:CoA-dependent acyltransferases
Superfamily:CoA-dependent acyltransferases
Family:Choline/Carnitine O-acyltransferase
55c3l7vA_
not modelled 10.1 13 PDB header:transcription
Chain: A: PDB Molecule:putative uncharacterized protein smu.1377c;
PDBTitle: crystal structure of a hypothetical protein smu.1377c from2 streptococcus mutans ua159
56d3broa1
not modelled 9.7 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
57d1u1qa_
not modelled 9.7 4 Fold:Ferredoxin-like
Superfamily:RNA-binding domain, RBD
Family:Canonical RBD
58c1xgwA_
not modelled 9.6 14 PDB header:endocytosis
Chain: A: PDB Molecule:epsin 4;
PDBTitle: the crystal structure of human enthoprotin n-terminal domain
59c3g3zA_
not modelled 9.4 19 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the structure of nmb1585, a marr family regulator from neisseria2 meningitidis
60d1qkia1
not modelled 9.3 19 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
61c3llkA_
not modelled 8.9 16 PDB header:oxidoreductase
Chain: A: PDB Molecule:sulfhydryl oxidase 1;
PDBTitle: sulfhydryl oxidase fragment of human qsox1
62c2pbrB_
not modelled 8.7 12 PDB header:transferase
Chain: B: PDB Molecule:thymidylate kinase;
PDBTitle: crystal structure of thymidylate kinase (aq_969) from aquifex aeolicus2 vf5
63c2qm6C_
not modelled 8.7 17 PDB header:transferase
Chain: C: PDB Molecule:gamma-glutamyltranspeptidase;
PDBTitle: crystal structure of helicobacter pylori gamma-glutamyltranspeptidase2 in complex with glutamate
64d1p4xa1
not modelled 8.5 7 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
65c2uxsA_
not modelled 8.4 14 PDB header:hydrolase
Chain: A: PDB Molecule:inorganic pyrophosphatase;
PDBTitle: 2.7a crystal structure of inorganic pyrophosphatase (rv3628)2 from mycobacterium tuberculosis at ph 7.5
66c3onlB_
not modelled 8.3 15 PDB header:protein transport
Chain: B: PDB Molecule:epsin-3;
PDBTitle: yeast ent3_enth-vti1p_habc complex structure
67d1y0ga_
not modelled 8.1 19 Fold:Streptavidin-like
Superfamily:YceI-like
Family:YceI-like
68d1r62a_
not modelled 8.1 19 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family:Histidine kinase
69d1mfra_
not modelled 8.0 15 Fold:Ferritin-like
Superfamily:Ferritin-like
Family:Ferritin
70d1eyha_
not modelled 8.0 14 Fold:alpha-alpha superhelix
Superfamily:ENTH/VHS domain
Family:ENTH domain
71d1z6om1
not modelled 8.0 24 Fold:Ferritin-like
Superfamily:Ferritin-like
Family:Ferritin
72c3iz5h_
not modelled 7.8 14 PDB header:ribosome
Chain: H: PDB Molecule:60s ribosomal protein l7a (l7ae);
PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome
73d2fbha1
not modelled 7.7 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
74d3c7ba2
not modelled 7.7 11 Fold:Ferredoxin-like
Superfamily:Nitrite/Sulfite reductase N-terminal domain-like
Family:DsrA/DsrB N-terminal-domain-like
75c4a1cX_
not modelled 7.7 18 PDB header:ribosome
Chain: X: PDB Molecule:60s ribosomal protein l32;
PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 4.
76d1udea_
not modelled 7.6 9 Fold:OB-fold
Superfamily:Inorganic pyrophosphatase
Family:Inorganic pyrophosphatase
77c3nnhA_
not modelled 7.5 15 PDB header:rna binding protein/rna
Chain: A: PDB Molecule:cugbp elav-like family member 1;
PDBTitle: crystal structure of the cugbp1 rrm1 with guuguuuuguuu rna
78c2adbA_
not modelled 7.5 14 PDB header:rna binding protein/rna
Chain: A: PDB Molecule:polypyrimidine tract-binding protein 1;
PDBTitle: solution structure of polypyrimidine tract binding protein2 rbd2 complexed with cucucu rna
79d1l3ka1
not modelled 7.4 4 Fold:Ferredoxin-like
Superfamily:RNA-binding domain, RBD
Family:Canonical RBD
80c2hvzA_
not modelled 7.4 14 PDB header:rna binding protein
Chain: A: PDB Molecule:splicing factor, arginine/serine-rich 7;
PDBTitle: solution structure of the rrm domain of sr rich factor 9g8
81d2ceia1
not modelled 7.4 19 Fold:Ferritin-like
Superfamily:Ferritin-like
Family:Ferritin
82d1zavz1
not modelled 7.3 32 Fold:Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Superfamily:Ribosomal protein L7/12, oligomerisation (N-terminal) domain
Family:Ribosomal protein L7/12, oligomerisation (N-terminal) domain
83c1zavZ_
not modelled 7.3 32 PDB header:structural protein
Chain: Z: PDB Molecule:50s ribosomal protein l7/l12;
PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p21
84c1zawZ_
not modelled 7.3 32 PDB header:structural protein
Chain: Z: PDB Molecule:50s ribosomal protein l7/l12;
PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p212121,2 form a
85c1zawX_
not modelled 7.2 30 PDB header:structural protein
Chain: X: PDB Molecule:50s ribosomal protein l7/l12;
PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p212121,2 form a
86c1zawY_
not modelled 7.2 30 PDB header:structural protein
Chain: Y: PDB Molecule:50s ribosomal protein l7/l12;
PDBTitle: ribosomal protein l10-l12(ntd) complex, space group p212121,2 form a
87d2za7a1
not modelled 7.2 16 Fold:Ferritin-like
Superfamily:Ferritin-like
Family:Ferritin
88c3ns5B_
not modelled 7.2 26 PDB header:translation
Chain: B: PDB Molecule:eukaryotic translation initiation factor 3 subunit b;
PDBTitle: crystal structure of the rna recognition motif of yeast eif3b residues2 76-161
89c1xl8B_
not modelled 7.1 14 PDB header:transferase
Chain: B: PDB Molecule:peroxisomal carnitine o-octanoyltransferase;
PDBTitle: crystal structure of mouse carnitine octanoyltransferase in2 complex with octanoylcarnitine
90d1whxa_
not modelled 7.1 29 Fold:Ferredoxin-like
Superfamily:RNA-binding domain, RBD
Family:Canonical RBD
91c2x3dC_
not modelled 7.0 14 PDB header:unknown function
Chain: C: PDB Molecule:sso6206;
PDBTitle: crystal structure of sso6206 from sulfolobus solfataricus p2
92c3lv8A_
not modelled 7.0 2 PDB header:transferase
Chain: A: PDB Molecule:thymidylate kinase;
PDBTitle: 1.8 angstrom resolution crystal structure of a thymidylate kinase2 (tmk) from vibrio cholerae o1 biovar eltor str. n16961 in complex3 with tmp, thymidine-5'-diphosphate and adp
93c2qy7A_
not modelled 7.0 12 PDB header:protein binding
Chain: A: PDB Molecule:clathrin interactor 1;
PDBTitle: crystal structure of human epsinr enth domain
94d1lnwa_
not modelled 7.0 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
95c2rs2A_
not modelled 6.9 9 PDB header:rna binding protein/rna
Chain: A: PDB Molecule:rna-binding protein musashi homolog 1;
PDBTitle: 1h, 13c, and 15n chemical shift assignments for musashi1 rbd1:r(guagu)2 complex
96c2fa5B_
not modelled 6.8 13 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator marr/emrr family;
PDBTitle: the crystal structure of an unliganded multiple antibiotic-2 resistance repressor (marr) from xanthomonas campestris
97c1ygaA_
not modelled 6.7 10 PDB header:isomerase
Chain: A: PDB Molecule:hypothetical 37.9 kda protein in bio3-hxt17
PDBTitle: crystal structure of saccharomyces cerevisiae yn9a protein,2 new york structural genomics consortium
98d1hsja1
not modelled 6.6 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
99c1qapA_
not modelled 6.6 16 PDB header:glycosyltransferase
Chain: A: PDB Molecule:quinolinic acid phosphoribosyltransferase;
PDBTitle: quinolinic acid phosphoribosyltransferase with bound2 quinolinic acid

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