Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP76102
DateThu Jan 5 12:18:56 GMT 2012
Unique Job ID51d59b7b115df24d

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1hk8a_
Top template information
Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:Class III anaerobic ribonucleotide reductase NRDD subunit
Confidence and coverage
Confidence: 95.0% Coverage: 13%
50 residues ( 13% of your sequence) have been modelled with 95.0% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

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















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Disorder  ??

























































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   .........70.........80.........90.........100.........110.........120
Sequence  QSLKDLERAYKNFFRKRAAFPRFKKRGQNDAFRYPQGVKLDQENSRIFLPKLGWMRYRNS
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?????
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   .........130.........140.........150.........160.........170.........180
Sequence  RQVTGVVKNVTVSQSCGKWYISIQTESEVSTPVHPSASMVGLDAGVAKLATLSDGTVFEP
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Disorder 
?































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






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??????????































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   .........250.........260.........270.........280.........290.........300
Sequence  HAMIVIEDLKVSNMSKSAAGTVSQPGRNVRAKSGLNRSILDQGWYEMRRQLAYKQLWRGG
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?????????????
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   .........310.........320.........330.........340.........350.........360
Sequence  QVLAVPPAYTSQRCAYCGHTAKENRLSQSKFRCQVCGYTANADVNGARNILAAGHAVLAC
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?
??






























????
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   .........370.........380..
Sequence  GEMVQSGRPLKQEPTEMIQATA
Secondary structure 















SS confidence 





















Disorder  ??????????????????????
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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 1hk8 chain A

3D model

Region: 283 - 337
Aligned: 50
Modelled: 53
Confidence: 95.0%
Identity: 20%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: Class III anaerobic ribonucleotide reductase NRDD subunit

Phyre2

PDB 1hk8 chain A

3D model

Region: 283 - 337
Aligned: 50
Modelled: 53
Confidence: 95.0%
Identity: 20%
PDB header:oxidoreductase
Chain: A: PDB Molecule:anaerobic ribonucleotide-triphosphate reductase;
PDBTitle: structural basis for allosteric substrate specificity2 regulation in class iii ribonucleotide reductases:3 nrdd in complex with dgtp

Phyre2

PDB 2gb5 chain B

3D model

Region: 310 - 340
Aligned: 30
Modelled: 31
Confidence: 94.7%
Identity: 23%
PDB header:hydrolase
Chain: B: PDB Molecule:nadh pyrophosphatase;
PDBTitle: crystal structure of nadh pyrophosphatase (ec 3.6.1.22) (1790429) from2 escherichia coli k12 at 2.30 a resolution

Phyre2

PDB 2qa4 chain Z

3D model

Region: 313 - 340
Aligned: 27
Modelled: 28
Confidence: 94.4%
Identity: 26%
PDB header:ribosome
Chain: Z: PDB Molecule:50s ribosomal protein l37ae;
PDBTitle: a more complete structure of the the l7/l12 stalk of the2 haloarcula marismortui 50s large ribosomal subunit

Phyre2

PDB 1yuz chain B

3D model

Region: 313 - 338
Aligned: 22
Modelled: 22
Confidence: 94.2%
Identity: 27%
PDB header:oxidoreductase
Chain: B: PDB Molecule:nigerythrin;
PDBTitle: partially reduced state of nigerythrin

Phyre2

PDB 1ffk chain W

3D model

Region: 313 - 340
Aligned: 27
Modelled: 28
Confidence: 94.1%
Identity: 41%
Fold: Rubredoxin-like
Superfamily: Zn-binding ribosomal proteins
Family: Ribosomal protein L37ae

Phyre2

PDB 1jj2 chain Y

3D model

Region: 313 - 340
Aligned: 27
Modelled: 28
Confidence: 94.1%
Identity: 33%
Fold: Rubredoxin-like
Superfamily: Zn-binding ribosomal proteins
Family: Ribosomal protein L37ae

Phyre2

PDB 1vqo chain Z domain 1

3D model

Region: 313 - 340
Aligned: 27
Modelled: 28
Confidence: 94.0%
Identity: 26%
Fold: Rubredoxin-like
Superfamily: Zn-binding ribosomal proteins
Family: Ribosomal protein L37ae

Phyre2

PDB 2zkr chain Z

3D model

Region: 313 - 340
Aligned: 27
Modelled: 28
Confidence: 93.9%
Identity: 30%
PDB header:ribosomal protein/rna
Chain: Z: PDB Molecule:e site t-rna;
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

Phyre2

PDB 1ysh chain D

3D model

Region: 313 - 340
Aligned: 27
Modelled: 28
Confidence: 93.9%
Identity: 26%
PDB header:structural protein/rna
Chain: D: PDB Molecule:ribosomal protein l37a;
PDBTitle: localization and dynamic behavior of ribosomal protein l30e

Phyre2

PDB 3cc4 chain Z

3D model

Region: 313 - 340
Aligned: 27
Modelled: 28
Confidence: 93.9%
Identity: 26%
PDB header:ribosome
Chain: Z: PDB Molecule:50s ribosomal protein l37ae;
PDBTitle: co-crystal structure of anisomycin bound to the 50s ribosomal subunit

Phyre2

PDB 4a17 chain Y

3D model

Region: 313 - 340
Aligned: 27
Modelled: 28
Confidence: 93.7%
Identity: 26%
PDB header:ribosome
Chain: Y: PDB Molecule:rpl37a;
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 2.

Phyre2

PDB 2akl chain A domain 2

3D model

Region: 314 - 347
Aligned: 32
Modelled: 34
Confidence: 93.6%
Identity: 13%
Fold: Rubredoxin-like
Superfamily: Zinc beta-ribbon
Family: PhnA zinc-binding domain

Phyre2

PDB 1s1i chain 9

3D model

Region: 313 - 340
Aligned: 27
Modelled: 28
Confidence: 93.5%
Identity: 26%
PDB header:ribosome
Chain: 9: PDB Molecule:60s ribosomal protein l43;
PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h.

Phyre2

PDB 2hr5 chain B

3D model

Region: 313 - 338
Aligned: 22
Modelled: 26
Confidence: 93.5%
Identity: 41%
PDB header:metal binding protein
Chain: B: PDB Molecule:rubrerythrin;
PDBTitle: pf1283- rubrerythrin from pyrococcus furiosus iron bound form

Phyre2

PDB 1pft chain A

3D model

Region: 311 - 341
Aligned: 31
Modelled: 31
Confidence: 93.1%
Identity: 19%
Fold: Rubredoxin-like
Superfamily: Zinc beta-ribbon
Family: Transcriptional factor domain

Phyre2

PDB 3jyw chain 9

3D model

Region: 313 - 340
Aligned: 27
Modelled: 28
Confidence: 92.9%
Identity: 26%
PDB header:ribosome
Chain: 9: PDB Molecule:60s ribosomal protein l43;
PDBTitle: structure of the 60s proteins for eukaryotic ribosome based on cryo-em2 map of thermomyces lanuginosus ribosome at 8.9a resolution

Phyre2

PDB 2akl chain A

3D model

Region: 314 - 343
Aligned: 28
Modelled: 30
Confidence: 92.5%
Identity: 14%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:phna-like protein pa0128;
PDBTitle: solution structure for phn-a like protein pa0128 from2 pseudomonas aeruginosa

Phyre2

PDB 1dl6 chain A

3D model

Region: 313 - 341
Aligned: 29
Modelled: 29
Confidence: 92.3%
Identity: 14%
Fold: Rubredoxin-like
Superfamily: Zinc beta-ribbon
Family: Transcriptional factor domain

Phyre2

PDB 2fiy chain A domain 1

3D model

Region: 307 - 341
Aligned: 33
Modelled: 35
Confidence: 92.2%
Identity: 15%
Fold: FdhE-like
Superfamily: FdhE-like
Family: FdhE-like

Phyre2

PDB 1kcf chain B

3D model

Region: 151 - 172
Aligned: 22
Modelled: 22
Confidence: 90.9%
Identity: 23%
PDB header:hydrolase
Chain: B: PDB Molecule:hypothetical 30.2 kd protein c25g10.02 in
PDBTitle: crystal structure of the yeast mitochondrial holliday2 junction resolvase, ydc2

Phyre2

PDB 1kcf chain A domain 2

3D model

Region: 156 - 172
Aligned: 17
Modelled: 17
Confidence: 87.1%
Identity: 18%
Fold: Ribonuclease H-like motif
Superfamily: Ribonuclease H-like
Family: Mitochondrial resolvase ydc2 catalytic domain

Phyre2

PDB 2owo chain A

3D model

Region: 312 - 362
Aligned: 49
Modelled: 49
Confidence: 72.4%
Identity: 18%
PDB header:ligase/dna
Chain: A: PDB Molecule:dna ligase;
PDBTitle: last stop on the road to repair: structure of e.coli dna ligase bound2 to nicked dna-adenylate

Phyre2

PDB 2zae chain B

3D model

Region: 216 - 339
Aligned: 82
Modelled: 82
Confidence: 55.2%
Identity: 23%
PDB header:hydrolase
Chain: B: PDB Molecule:ribonuclease p protein component 4;
PDBTitle: crystal structure of protein ph1601p in complex with protein ph1771p2 of archaeal ribonuclease p from pyrococcus horikoshii ot3

Phyre2
1

d1hk8a_
2

c1hk8A_
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c2gb5B_
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c2qa4Z_
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c1yuzB_
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d1ffkw_
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d1jj2y_
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d1vqoz1
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c2zkrz_
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c1yshD_
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c3cc4Z_
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c4a17Y_
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d2akla2
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c1s1i9_
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c2hr5B_
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d1pfta_
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c3jyw9_
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c2aklA_
19

d1dl6a_
20

d2fiya1
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c1kcfB_
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d1kcfa2
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c2owoA_
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c2zaeB_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1hk8a_



95.0 20 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:Class III anaerobic ribonucleotide reductase NRDD subunit
2c1hk8A_



95.0 20 PDB header:oxidoreductase
Chain: A: PDB Molecule:anaerobic ribonucleotide-triphosphate reductase;
PDBTitle: structural basis for allosteric substrate specificity2 regulation in class iii ribonucleotide reductases:3 nrdd in complex with dgtp
3c2gb5B_



94.7 23 PDB header:hydrolase
Chain: B: PDB Molecule:nadh pyrophosphatase;
PDBTitle: crystal structure of nadh pyrophosphatase (ec 3.6.1.22) (1790429) from2 escherichia coli k12 at 2.30 a resolution
4c2qa4Z_



94.4 26 PDB header:ribosome
Chain: Z: PDB Molecule:50s ribosomal protein l37ae;
PDBTitle: a more complete structure of the the l7/l12 stalk of the2 haloarcula marismortui 50s large ribosomal subunit
5c1yuzB_



94.2 27 PDB header:oxidoreductase
Chain: B: PDB Molecule:nigerythrin;
PDBTitle: partially reduced state of nigerythrin
6d1ffkw_



94.1 41 Fold:Rubredoxin-like
Superfamily:Zn-binding ribosomal proteins
Family:Ribosomal protein L37ae
7d1jj2y_



94.1 33 Fold:Rubredoxin-like
Superfamily:Zn-binding ribosomal proteins
Family:Ribosomal protein L37ae
8d1vqoz1



94.0 26 Fold:Rubredoxin-like
Superfamily:Zn-binding ribosomal proteins
Family:Ribosomal protein L37ae
9c2zkrz_



93.9 30 PDB header:ribosomal protein/rna
Chain: Z: PDB Molecule:e site t-rna;
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
10c1yshD_



93.9 26 PDB header:structural protein/rna
Chain: D: PDB Molecule:ribosomal protein l37a;
PDBTitle: localization and dynamic behavior of ribosomal protein l30e
11c3cc4Z_



93.9 26 PDB header:ribosome
Chain: Z: PDB Molecule:50s ribosomal protein l37ae;
PDBTitle: co-crystal structure of anisomycin bound to the 50s ribosomal subunit
12c4a17Y_



93.7 26 PDB header:ribosome
Chain: Y: PDB Molecule:rpl37a;
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 2.
13d2akla2



93.6 13 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:PhnA zinc-binding domain
14c1s1i9_



93.5 26 PDB header:ribosome
Chain: 9: PDB Molecule:60s ribosomal protein l43;
PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h.
15c2hr5B_



93.5 41 PDB header:metal binding protein
Chain: B: PDB Molecule:rubrerythrin;
PDBTitle: pf1283- rubrerythrin from pyrococcus furiosus iron bound form
16d1pfta_



93.1 19 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
17c3jyw9_



92.9 26 PDB header:ribosome
Chain: 9: PDB Molecule:60s ribosomal protein l43;
PDBTitle: structure of the 60s proteins for eukaryotic ribosome based on cryo-em2 map of thermomyces lanuginosus ribosome at 8.9a resolution
18c2aklA_



92.5 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:phna-like protein pa0128;
PDBTitle: solution structure for phn-a like protein pa0128 from2 pseudomonas aeruginosa
19d1dl6a_



92.3 14 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
20d2fiya1



92.2 15 Fold:FdhE-like
Superfamily:FdhE-like
Family:FdhE-like
21c2opfA_



not modelled 92.1 28 PDB header:hydrolase/dna
Chain: A: PDB Molecule:endonuclease viii;
PDBTitle: crystal structure of the dna repair enzyme endonuclease-viii (nei)2 from e. coli (r252a) in complex with ap-site containing dna substrate
22c2lcqA_



not modelled 91.5 15 PDB header:metal binding protein
Chain: A: PDB Molecule:putative toxin vapc6;
PDBTitle: solution structure of the endonuclease nob1 from p.horikoshii
23c1ee8A_



not modelled 91.4 20 PDB header:dna binding protein
Chain: A: PDB Molecule:mutm (fpg) protein;
PDBTitle: crystal structure of mutm (fpg) protein from thermus thermophilus hb8
24c2f5qA_



not modelled 91.4 20 PDB header:hydrolase/dna
Chain: A: PDB Molecule:formamidopyrimidine-dna glycosidase;
PDBTitle: catalytically inactive (e3q) mutm crosslinked to oxog:c2 containing dna cc2
25c1nnjA_



not modelled 91.2 24 PDB header:hydrolase
Chain: A: PDB Molecule:formamidopyrimidine-dna glycosylase;
PDBTitle: crystal structure complex between the lactococcus lactis fpg and an2 abasic site containing dna
26c3ky9B_



not modelled 91.1 16 PDB header:apoptosis
Chain: B: PDB Molecule:proto-oncogene vav;
PDBTitle: autoinhibited vav1
27c3k7aM_



not modelled 91.0 23 PDB header:transcription
Chain: M: PDB Molecule:transcription initiation factor iib;
PDBTitle: crystal structure of an rna polymerase ii-tfiib complex
28c1kcfB_



90.9 23 PDB header:hydrolase
Chain: B: PDB Molecule:hypothetical 30.2 kd protein c25g10.02 in
PDBTitle: crystal structure of the yeast mitochondrial holliday2 junction resolvase, ydc2
29c1k82D_



not modelled 90.8 28 PDB header:hydrolase/dna
Chain: D: PDB Molecule:formamidopyrimidine-dna glycosylase;
PDBTitle: crystal structure of e.coli formamidopyrimidine-dna2 glycosylase (fpg) covalently trapped with dna
30c1dvbA_



not modelled 90.6 26 PDB header:electron transport
Chain: A: PDB Molecule:rubrerythrin;
PDBTitle: rubrerythrin
31c3cngC_



not modelled 90.5 17 PDB header:hydrolase
Chain: C: PDB Molecule:nudix hydrolase;
PDBTitle: crystal structure of nudix hydrolase from nitrosomonas europaea
32d1twfi2



not modelled 90.4 18 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
33c3bjiA_



not modelled 89.9 17 PDB header:signaling protein
Chain: A: PDB Molecule:proto-oncogene vav;
PDBTitle: structural basis of promiscuous guanine nucleotide exchange2 by the t-cell essential vav1
34c2vrwB_



not modelled 89.2 16 PDB header:signaling protein
Chain: B: PDB Molecule:proto-oncogene vav;
PDBTitle: critical structural role for the ph and c1 domains of the2 vav1 exchange factor
35c1y1yS_



not modelled 89.1 18 PDB header:transferase/transcription/dna-rna hybrid
Chain: S: PDB Molecule:transcription elongation factor s-ii;
PDBTitle: rna polymerase ii-tfiis-dna/rna complex
36c1i3qI_



not modelled 89.0 24 PDB header:transcription
Chain: I: PDB Molecule:dna-directed rna polymerase ii 14.2kd
PDBTitle: rna polymerase ii crystal form i at 3.1 a resolution
37c3ndjA_



not modelled 88.2 31 PDB header:transferase
Chain: A: PDB Molecule:methyltransferase;
PDBTitle: x-ray structure of a c-3'-methyltransferase in complex with s-2 adenosyl-l-homocysteine and sugar product
38d1kcfa2



87.1 18 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Mitochondrial resolvase ydc2 catalytic domain
39c3pfqA_



not modelled 87.0 21 PDB header:transferase
Chain: A: PDB Molecule:protein kinase c beta type;
PDBTitle: crystal structure and allosteric activation of protein kinase c beta2 ii
40c1pqvS_



not modelled 87.0 19 PDB header:transferase/transcription
Chain: S: PDB Molecule:transcription elongation factor s-ii;
PDBTitle: rna polymerase ii-tfiis complex
41d1tdza3



not modelled 86.9 26 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
42d1ee8a3



not modelled 86.6 20 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
43d1k3xa3



not modelled 86.3 28 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
44d1r2za3



not modelled 85.7 20 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
45d1l1ta3



not modelled 85.6 20 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
46c2f9iD_



not modelled 85.2 19 PDB header:transferase
Chain: D: PDB Molecule:acetyl-coenzyme a carboxylase carboxyl
PDBTitle: crystal structure of the carboxyltransferase subunit of acc2 from staphylococcus aureus
47d1k82a3



not modelled 85.0 28 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
48c2k5cA_



not modelled 84.7 36 PDB header:metal binding protein
Chain: A: PDB Molecule:uncharacterized protein pf0385;
PDBTitle: nmr structure for pf0385
49d1yuza2



not modelled 84.6 27 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
50c2f9yB_



not modelled 84.6 24 PDB header:ligase
Chain: B: PDB Molecule:acetyl-coenzyme a carboxylase carboxyl transferase subunit
PDBTitle: the crystal structure of the carboxyltransferase subunit of acc from2 escherichia coli
51d2f9yb1



not modelled 84.6 24 Fold:ClpP/crotonase
Superfamily:ClpP/crotonase
Family:Biotin dependent carboxylase carboxyltransferase domain
52d1nnqa2



not modelled 84.3 41 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
53c2qkdA_



not modelled 84.2 28 PDB header:signaling protein, cell cycle
Chain: A: PDB Molecule:zinc finger protein zpr1;
PDBTitle: crystal structure of tandem zpr1 domains
54d1qypa_



not modelled 84.0 36 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
55d1tfia_



not modelled 83.6 29 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
56c3zyqA_



not modelled 83.6 22 PDB header:signaling
Chain: A: PDB Molecule:hepatocyte growth factor-regulated tyrosine kinase
PDBTitle: crystal structure of the tandem vhs and fyve domains of hepatocyte2 growth factor-regulated tyrosine kinase substrate (hgs-hrs) at 1.483 a resolution
57c1nuiA_



not modelled 82.8 23 PDB header:replication
Chain: A: PDB Molecule:dna primase/helicase;
PDBTitle: crystal structure of the primase fragment of bacteriophage t7 primase-2 helicase protein
58c3h0gI_



not modelled 82.7 22 PDB header:transcription
Chain: I: PDB Molecule:dna-directed rna polymerase ii subunit rpb9;
PDBTitle: rna polymerase ii from schizosaccharomyces pombe
59c1dvpA_



not modelled 82.6 24 PDB header:transferase
Chain: A: PDB Molecule:hepatocyte growth factor-regulated tyrosine
PDBTitle: crystal structure of the vhs and fyve tandem domains of hrs,2 a protein involved in membrane trafficking and signal3 transduction
60c3na7A_



not modelled 82.4 21 PDB header:gene regulation, chaperone
Chain: A: PDB Molecule:hp0958;
PDBTitle: 2.2 angstrom structure of the hp0958 protein from helicobacter pylori2 ccug 17874
61d1iv0a_



not modelled 81.4 21 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Putative Holliday junction resolvase RuvX
62d1nu0a_



not modelled 81.4 11 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Putative Holliday junction resolvase RuvX
63d1lkoa2



not modelled 80.8 26 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
64d1vm9a_



not modelled 80.5 15 Fold:ISP domain
Superfamily:ISP domain
Family:Rieske iron-sulfur protein (ISP)
65d2k4xa1



not modelled 80.1 35 Fold:Rubredoxin-like
Superfamily:Zn-binding ribosomal proteins
Family:Ribosomal protein S27a
66c2kdxA_



not modelled 79.0 30 PDB header:metal-binding protein
Chain: A: PDB Molecule:hydrogenase/urease nickel incorporation protein
PDBTitle: solution structure of hypa protein
67d1pfva3



not modelled 78.3 30 Fold:Rubredoxin-like
Superfamily:Methionyl-tRNA synthetase (MetRS), Zn-domain
Family:Methionyl-tRNA synthetase (MetRS), Zn-domain
68d2ct7a1



not modelled 78.2 29 Fold:RING/U-box
Superfamily:RING/U-box
Family:IBR domain
69d2j0151



not modelled 77.8 30 Fold:Rubredoxin-like
Superfamily:Zn-binding ribosomal proteins
Family:Ribosomal protein L32p
70c1z2qA_



not modelled 76.8 23 PDB header:membrane protein
Chain: A: PDB Molecule:lm5-1;
PDBTitle: high-resolution solution structure of the lm5-1 fyve domain2 from leishmania major
71c3gn5B_



not modelled 75.9 18 PDB header:dna binding protein
Chain: B: PDB Molecule:hth-type transcriptional regulator mqsa (ygit/b3021);
PDBTitle: structure of the e. coli protein mqsa (ygit/b3021)
72d2zjrz1



not modelled 75.5 36 Fold:Rubredoxin-like
Superfamily:Zn-binding ribosomal proteins
Family:Ribosomal protein L32p
73d1tbna_



not modelled 74.4 15 Fold:Cysteine-rich domain
Superfamily:Cysteine-rich domain
Family:Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)
74c1jocA_



not modelled 73.6 26 PDB header:membrane protein
Chain: A: PDB Molecule:early endosomal autoantigen 1;
PDBTitle: eea1 homodimer of c-terminal fyve domain bound to inositol2 1,3-diphosphate
75d1vhxa_



not modelled 73.4 7 Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Putative Holliday junction resolvase RuvX
76d1wiia_



not modelled 73.1 23 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Putative zinc binding domain
77c2owoA_



72.4 18 PDB header:ligase/dna
Chain: A: PDB Molecule:dna ligase;
PDBTitle: last stop on the road to repair: structure of e.coli dna ligase bound2 to nicked dna-adenylate
78c2rowA_



not modelled 72.4 14 PDB header:transferase
Chain: A: PDB Molecule:rho-associated protein kinase 2;
PDBTitle: the c1 domain of rock ii
79c2e9hA_



not modelled 72.4 23 PDB header:translation
Chain: A: PDB Molecule:eukaryotic translation initiation factor 5;
PDBTitle: solution structure of the eif-5_eif-2b domain from human2 eukaryotic translation initiation factor 5
80c2ba1B_



not modelled 72.1 22 PDB header:rna binding protein
Chain: B: PDB Molecule:archaeal exosome rna binding protein csl4;
PDBTitle: archaeal exosome core
81c3t7lA_



not modelled 72.0 18 PDB header:transport protein
Chain: A: PDB Molecule:zinc finger fyve domain-containing protein 16;
PDBTitle: crystal structure of the fyve domain of endofin (zfyve16) at 1.1a2 resolution
82c3a44D_



not modelled 71.6 24 PDB header:metal binding protein
Chain: D: PDB Molecule:hydrogenase nickel incorporation protein hypa;
PDBTitle: crystal structure of hypa in the dimeric form
83d1ptqa_



not modelled 71.0 21 Fold:Cysteine-rich domain
Superfamily:Cysteine-rich domain
Family:Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)
84d1joca1



not modelled 71.0 26 Fold:FYVE/PHD zinc finger
Superfamily:FYVE/PHD zinc finger
Family:FYVE, a phosphatidylinositol-3-phosphate binding domain
85c2enzA_



not modelled 70.7 21 PDB header:transferase
Chain: A: PDB Molecule:protein kinase c theta type;
PDBTitle: solution structure of the second c1 domain from human2 protein kinase c theta
86d1vd4a_



not modelled 70.3 29 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
87c1y8fA_



not modelled 70.0 21 PDB header:endocytosis/exocytosis,signaling protein
Chain: A: PDB Molecule:unc-13 homolog a;
PDBTitle: solution structure of the munc13-1 c1-domain
88d1l1oc_



not modelled 69.8 17 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
89c2eliA_



not modelled 69.8 16 PDB header:transferase
Chain: A: PDB Molecule:protein kinase c alpha type;
PDBTitle: solution structure of the second phorbol2 esters/diacylglycerol binding domain of human protein3 kinase c alpha type
90d1p91a_



not modelled 69.7 17 Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:rRNA methyltransferase RlmA
91d1x3za1



not modelled 68.9 37 Fold:Cysteine proteinases
Superfamily:Cysteine proteinases
Family:Transglutaminase core
92d2j9ub1



not modelled 68.9 26 Fold:Rubredoxin-like
Superfamily:Ran binding protein zinc finger-like
Family:Ran binding protein zinc finger-like
93c2j9uB_



not modelled 68.9 26 PDB header:protein transport
Chain: B: PDB Molecule:vacuolar protein sorting-associated protein 36;
PDBTitle: 2 angstrom x-ray structure of the yeast escrt-i vps28 c-2 terminus in complex with the nzf-n domain from escrt-ii
94d1wffa_



not modelled 68.6 38 Fold:AN1-like Zinc finger
Superfamily:AN1-like Zinc finger
Family:AN1-like Zinc finger
95c2dcuB_



not modelled 67.9 22 PDB header:translation
Chain: B: PDB Molecule:translation initiation factor 2 beta subunit;
PDBTitle: crystal structure of translation initiation factor aif2betagamma2 heterodimer with gdp
96c2nn6I_



not modelled 67.9 7 PDB header:hydrolase/transferase
Chain: I: PDB Molecule:3'-5' exoribonuclease csl4 homolog;
PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40
97c3cw2M_



not modelled 67.9 19 PDB header:translation
Chain: M: PDB Molecule:translation initiation factor 2 subunit beta;
PDBTitle: crystal structure of the intact archaeal translation2 initiation factor 2 from sulfolobus solfataricus .
98d1xa6a3



not modelled 67.8 23 Fold:Cysteine-rich domain
Superfamily:Cysteine-rich domain
Family:Protein kinase cysteine-rich domain (cys2, phorbol-binding domain)
99c2i7fB_



not modelled 67.4 15 PDB header:oxidoreductase
Chain: B: PDB Molecule:ferredoxin component of dioxygenase;
PDBTitle: sphingomonas yanoikuyae b1 ferredoxin
100d1k81a_



not modelled 67.3 22 Fold:Zinc-binding domain of translation initiation factor 2 beta
Superfamily:Zinc-binding domain of translation initiation factor 2 beta
Family:Zinc-binding domain of translation initiation factor 2 beta
101c3dqyA_



not modelled 67.1 11 PDB header:oxidoreductase
Chain: A: PDB Molecule:toluene 1,2-dioxygenase system ferredoxin
PDBTitle: crystal structure of toluene 2,3-dioxygenase ferredoxin
102c2de7E_



not modelled 65.5 19 PDB header:oxidoreductase
Chain: E: PDB Molecule:ferredoxin component of carbazole;
PDBTitle: the substrate-bound complex between oxygenase and2 ferredoxin in carbazole 1,9a-dioxygenase
103d1dgsa1



not modelled 65.4 29 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:NAD+-dependent DNA ligase, domain 3
104c2ennA_



not modelled 65.3 13 PDB header:transferase
Chain: A: PDB Molecule:protein kinase c theta type;
PDBTitle: solution structure of the first c1 domain from human2 protein kinase c theta
105c2js4A_



not modelled 64.8 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:upf0434 protein bb2007;
PDBTitle: solution nmr structure of bordetella bronchiseptica protein2 bb2007. northeast structural genomics consortium target3 bor54
106c1neeA_



not modelled 64.8 22 PDB header:translation
Chain: A: PDB Molecule:probable translation initiation factor 2 beta
PDBTitle: structure of archaeal translation factor aif2beta from2 methanobacterium thermoautrophicum
107c1dgsB_



not modelled 64.8 24 PDB header:ligase
Chain: B: PDB Molecule:dna ligase;
PDBTitle: crystal structure of nad+-dependent dna ligase from t.2 filiformis
108c3egxB_



not modelled 64.5 24 PDB header:protein transport
Chain: B: PDB Molecule:protein transport protein sec24a;
PDBTitle: crystal structure of the mammalian copii-coat protein2 sec23a/24a complexed with the snare protein sec22b and3 bound to the transport signal sequence of the snare protein4 bet1
109c1p84E_



not modelled 64.1 12 PDB header:oxidoreductase
Chain: E: PDB Molecule:ubiquinol-cytochrome c reductase iron-sulfur
PDBTitle: hdbt inhibited yeast cytochrome bc1 complex
110d1wfpa_



not modelled 64.0 41 Fold:AN1-like Zinc finger
Superfamily:AN1-like Zinc finger
Family:AN1-like Zinc finger
111d1pvma3



not modelled 64.0 35 Fold:Rubredoxin-like
Superfamily:Hypothetical protein Ta0289 C-terminal domain
Family:Hypothetical protein Ta0289 C-terminal domain
112c2e73A_



not modelled 64.0 17 PDB header:transferase
Chain: A: PDB Molecule:protein kinase c gamma type;
PDBTitle: solution structure of the phorbol esters/diacylglycerol2 binding domain of protein kinase c gamma
113c3bvoA_



not modelled 64.0 31 PDB header:chaperone
Chain: A: PDB Molecule:co-chaperone protein hscb, mitochondrial precursor;
PDBTitle: crystal structure of human co-chaperone protein hscb
114c2gajA_



not modelled 63.4 23 PDB header:isomerase
Chain: A: PDB Molecule:dna topoisomerase i;
PDBTitle: structure of full length topoisomerase i from thermotoga maritima in2 monoclinic crystal form
115c1x4uA_



not modelled 63.2 19 PDB header:lipid binding protein
Chain: A: PDB Molecule:zinc finger, fyve domain containing 27 isoform b;
PDBTitle: solution structure of the fyve domain from human fyve2 domain containing 27 isoform b protein
116c3eswA_



not modelled 63.0 33 PDB header:hydrolase
Chain: A: PDB Molecule:peptide-n(4)-(n-acetyl-beta-glucosaminyl)asparagine
PDBTitle: complex of yeast pngase with glcnac2-iac.
117c2jr6A_



not modelled 62.9 4 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:upf0434 protein nma0874;
PDBTitle: solution structure of upf0434 protein nma0874. northeast structural2 genomics target mr32
118c2pziA_



not modelled 62.4 25 PDB header:transferase
Chain: A: PDB Molecule:probable serine/threonine-protein kinase pkng;
PDBTitle: crystal structure of protein kinase pkng from mycobacterium2 tuberculosis in complex with tetrahydrobenzothiophene ax20017
119c2e76D_



not modelled 62.4 22 PDB header:photosynthesis
Chain: D: PDB Molecule:cytochrome b6-f complex iron-sulfur subunit;
PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus
120d1d0qa_



not modelled 62.0 25 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:DNA primase zinc finger

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