Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP28903
DateThu Jan 5 11:45:16 GMT 2012
Unique Job IDa3d84c41e8b53620

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1hk8A_
Top template information
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
Confidence and coverage
Confidence:100.0% Coverage: 78%
555 residues ( 78% 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.
678 residues ( 95%) 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  MTPHVMKRDGCKVPFKSERIKEAILRAAKAAEVDDADYCATVAAVVSEQMQGRNQVDINE
Secondary structure 
SS confidence 
Disorder  ???
?
?????
???
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  IQTAVENQLMSGPYKQLARAYIEYRHDRDIEREKRGRLNQEIRGLVEQTNASLLNENANK
Secondary structure 
SS confidence 
Disorder 
??
????
?????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  DSKVIPTQRDLLAGIVAKHYARQHLLPRDVVQAHERGDIHYHDLDYSPFFPMFNCMLIDL
Secondary structure 
SS confidence 
Disorder  ???????
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  KGMLTQGFKMGNAEIEPPKSISTATAVTAQIIAQVASHIYGGTTINRIDEVLAPFVTASY
Secondary structure 
SS confidence 
Disorder 
????????
?
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  NKHRKTAEEWNIPDAEGYANSRTIKECYDAFQSLEYEVNTLHTANGQTPFVTFGFGLGTS
Secondary structure 
SS confidence 
Disorder  ?
?
???
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  WESRLIQESILRNRIAGLGKNRKTAVFPKLVFAIRDGLNHKKGDPNYDIKQLALECASKR
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  MYPDILNYDQVVKVTGSFKTPMGCRSFLGVWENENGEQIHDGRNNLGVISLNLPRIALEA
Secondary structure 
SS confidence 
Disorder 
?
????
????
??
?
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  KGDEATFWKLLDERLVLARKALMTRIARLEGVKARVAPILYMEGACGVRLNADDDVSEIF
Secondary structure 
SS confidence 
Disorder 
?????
?
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  KNGRASISLGYIGIHETINALFGGEHVYDNEQLRAKGIAIVERLRQAVDQWKEETGYGFS
Secondary structure 
SS confidence 
Disorder 
??????
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  LYSTPSENLCDRFCRLDTAEFGVVPGVTDKGYYTNSFHLDVEKKVNPYDKIDFEAPYPPL
Secondary structure 
SS confidence 
Disorder 
??
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  ANGGFICYGEYPNIQHNLKALEDVWDYSYQHVPYYGTNTPIDECYECGFTGEFECTSKGF
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........670.........680.........690.........700.........710..
Sequence  TCPKCGNHDASRVSVTRRVCGYLGSPDARPFNAGKQEEVKRRVKHLGNGQIG
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 1hk8 chain A

3D model

Region: 121 - 687
Aligned: 555
Modelled: 567
Confidence: 100.0%
Identity: 57%
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 1hk8 chain A

3D model

Region: 121 - 687
Aligned: 555
Modelled: 567
Confidence: 100.0%
Identity: 57%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: Class III anaerobic ribonucleotide reductase NRDD subunit

Phyre2

PDB 3r1r chain B

3D model

Region: 4 - 534
Aligned: 470
Modelled: 496
Confidence: 99.9%
Identity: 13%
PDB header:complex (oxidoreductase/peptide)
Chain: B: PDB Molecule:ribonucleotide reductase r1 protein;
PDBTitle: ribonucleotide reductase r1 protein with amppnp occupying2 the activity site from escherichia coli

Phyre2

PDB 3hnf chain A

3D model

Region: 18 - 632
Aligned: 530
Modelled: 582
Confidence: 99.8%
Identity: 14%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large subunit;
PDBTitle: crystal structure of human ribonucleotide reductase 1 bound to the2 effectors ttp and datp

Phyre2

PDB 2cvu chain A

3D model

Region: 75 - 632
Aligned: 480
Modelled: 517
Confidence: 99.8%
Identity: 15%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large chain
PDBTitle: structures of yeast ribonucleotide reductase i

Phyre2

PDB 2wgh chain A

3D model

Region: 23 - 632
Aligned: 515
Modelled: 538
Confidence: 99.8%
Identity: 14%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large
PDBTitle: human ribonucleotide reductase r1 subunit (rrm1) in complex2 with datp and mg.

Phyre2

PDB 1xje chain A

3D model

Region: 89 - 632
Aligned: 481
Modelled: 518
Confidence: 99.7%
Identity: 14%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleotide reductase, b12-dependent;
PDBTitle: structural mechanism of allosteric substrate specificity in a2 ribonucleotide reductase: dttp-gdp complex

Phyre2

PDB 1pem chain A

3D model

Region: 21 - 534
Aligned: 437
Modelled: 493
Confidence: 99.6%
Identity: 15%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase 2 alpha
PDBTitle: ribonucleotide reductase protein r1e from salmonella2 typhimurium

Phyre2

PDB 1r9d chain A

3D model

Region: 195 - 705
Aligned: 430
Modelled: 475
Confidence: 99.5%
Identity: 18%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: PFL-like

Phyre2

PDB 1h16 chain A

3D model

Region: 180 - 707
Aligned: 440
Modelled: 462
Confidence: 99.3%
Identity: 16%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: PFL-like

Phyre2

PDB 2f3o chain B

3D model

Region: 196 - 638
Aligned: 384
Modelled: 422
Confidence: 99.3%
Identity: 18%
PDB header:unknown function
Chain: B: PDB Molecule:pyruvate formate-lyase 2;
PDBTitle: crystal structure of a glycyl radical enzyme from archaeoglobus2 fulgidus

Phyre2

PDB 1l1l chain A

3D model

Region: 163 - 642
Aligned: 410
Modelled: 447
Confidence: 99.3%
Identity: 13%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: B12-dependent (class II) ribonucleotide reductase

Phyre2

PDB 1peq chain A domain 2

3D model

Region: 184 - 632
Aligned: 392
Modelled: 427
Confidence: 99.1%
Identity: 14%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: R1 subunit of ribonucleotide reductase, C-terminal domain

Phyre2

PDB 2y8n chain C

3D model

Region: 195 - 638
Aligned: 397
Modelled: 422
Confidence: 98.9%
Identity: 16%
PDB header:lyase
Chain: C: PDB Molecule:4-hydroxyphenylacetate decarboxylase large subunit;
PDBTitle: crystal structure of glycyl radical enzyme

Phyre2

PDB 1rlr chain A domain 2

3D model

Region: 184 - 534
Aligned: 304
Modelled: 325
Confidence: 98.8%
Identity: 15%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: R1 subunit of ribonucleotide reductase, C-terminal domain

Phyre2

PDB 1qhm chain A

3D model

Region: 180 - 545
Aligned: 312
Modelled: 329
Confidence: 98.8%
Identity: 15%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: PFL-like

Phyre2

PDB 1rlr chain A domain 1

3D model

Region: 8 - 179
Aligned: 162
Modelled: 172
Confidence: 98.7%
Identity: 12%
Fold: R1 subunit of ribonucleotide reductase, N-terminal domain
Superfamily: R1 subunit of ribonucleotide reductase, N-terminal domain
Family: R1 subunit of ribonucleotide reductase, N-terminal domain

Phyre2

PDB 3a44 chain D

3D model

Region: 607 - 671
Aligned: 63
Modelled: 65
Confidence: 96.0%
Identity: 17%
PDB header:metal binding protein
Chain: D: PDB Molecule:hydrogenase nickel incorporation protein hypa;
PDBTitle: crystal structure of hypa in the dimeric form

Phyre2

PDB 2kdx chain A

3D model

Region: 607 - 671
Aligned: 63
Modelled: 65
Confidence: 95.9%
Identity: 11%
PDB header:metal-binding protein
Chain: A: PDB Molecule:hydrogenase/urease nickel incorporation protein
PDBTitle: solution structure of hypa protein

Phyre2

PDB 1dvb chain A

3D model

Region: 619 - 668
Aligned: 46
Modelled: 50
Confidence: 95.1%
Identity: 20%
PDB header:electron transport
Chain: A: PDB Molecule:rubrerythrin;
PDBTitle: rubrerythrin

Phyre2
1
c1hk8A_
2
d1hk8a_
3
c3r1rB_
4
c3hnfA_
5
c2cvuA_
6
c2wghA_
7
c1xjeA_
8
c1pemA_
9
d1r9da_
10
d1h16a_
11
c2f3oB_
12
d1l1la_
13
d1peqa2
14
c2y8nC_
15
d1rlra2
16
d1qhma_
17
d1rlra1
18
c3a44D_
19
c2kdxA_
20
c1dvbA_
21
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24
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1hk8A_
100.0 57 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
2d1hk8a_
100.0 57 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:Class III anaerobic ribonucleotide reductase NRDD subunit
3c3r1rB_
99.9 13 PDB header:complex (oxidoreductase/peptide)
Chain: B: PDB Molecule:ribonucleotide reductase r1 protein;
PDBTitle: ribonucleotide reductase r1 protein with amppnp occupying2 the activity site from escherichia coli
4c3hnfA_
99.8 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large subunit;
PDBTitle: crystal structure of human ribonucleotide reductase 1 bound to the2 effectors ttp and datp
5c2cvuA_
99.8 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large chain
PDBTitle: structures of yeast ribonucleotide reductase i
6c2wghA_
99.8 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large
PDBTitle: human ribonucleotide reductase r1 subunit (rrm1) in complex2 with datp and mg.
7c1xjeA_
99.7 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleotide reductase, b12-dependent;
PDBTitle: structural mechanism of allosteric substrate specificity in a2 ribonucleotide reductase: dttp-gdp complex
8c1pemA_
99.6 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase 2 alpha
PDBTitle: ribonucleotide reductase protein r1e from salmonella2 typhimurium
9d1r9da_
99.5 18 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
10d1h16a_
99.3 16 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
11c2f3oB_
99.3 18 PDB header:unknown function
Chain: B: PDB Molecule:pyruvate formate-lyase 2;
PDBTitle: crystal structure of a glycyl radical enzyme from archaeoglobus2 fulgidus
12d1l1la_
99.3 13 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:B12-dependent (class II) ribonucleotide reductase
13d1peqa2
99.1 14 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:R1 subunit of ribonucleotide reductase, C-terminal domain
14c2y8nC_
98.9 16 PDB header:lyase
Chain: C: PDB Molecule:4-hydroxyphenylacetate decarboxylase large subunit;
PDBTitle: crystal structure of glycyl radical enzyme
15d1rlra2
98.8 15 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:R1 subunit of ribonucleotide reductase, C-terminal domain
16d1qhma_
98.8 15 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
17d1rlra1
98.7 12 Fold:R1 subunit of ribonucleotide reductase, N-terminal domain
Superfamily:R1 subunit of ribonucleotide reductase, N-terminal domain
Family:R1 subunit of ribonucleotide reductase, N-terminal domain
18c3a44D_
96.0 17 PDB header:metal binding protein
Chain: D: PDB Molecule:hydrogenase nickel incorporation protein hypa;
PDBTitle: crystal structure of hypa in the dimeric form
19c2kdxA_
95.9 11 PDB header:metal-binding protein
Chain: A: PDB Molecule:hydrogenase/urease nickel incorporation protein
PDBTitle: solution structure of hypa protein
20c1dvbA_
95.1 20 PDB header:electron transport
Chain: A: PDB Molecule:rubrerythrin;
PDBTitle: rubrerythrin
21c1yuzB_
not modelled 94.1 26 PDB header:oxidoreductase
Chain: B: PDB Molecule:nigerythrin;
PDBTitle: partially reduced state of nigerythrin
22c2hr5B_
not modelled 93.8 30 PDB header:metal binding protein
Chain: B: PDB Molecule:rubrerythrin;
PDBTitle: pf1283- rubrerythrin from pyrococcus furiosus iron bound form
23d2gmga1
not modelled 89.2 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:PF0610-like
24c2lcqA_
not modelled 88.3 38 PDB header:metal binding protein
Chain: A: PDB Molecule:putative toxin vapc6;
PDBTitle: solution structure of the endonuclease nob1 from p.horikoshii
25d1lkoa2
not modelled 85.6 33 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
26d1yuza2
not modelled 85.1 29 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
27c3lpeF_
not modelled 84.8 27 PDB header:transferase
Chain: F: PDB Molecule:dna-directed rna polymerase subunit e'';
PDBTitle: crystal structure of spt4/5ngn heterodimer complex from methanococcus2 jannaschii
28d1nnqa2
not modelled 84.6 30 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
29d1ryqa_
not modelled 82.5 28 Fold:Rubredoxin-like
Superfamily:RNA polymerase subunits
Family:RpoE2-like
30d1dx8a_
not modelled 82.2 40 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
31d2j0151
not modelled 82.0 30 Fold:Rubredoxin-like
Superfamily:Zn-binding ribosomal proteins
Family:Ribosomal protein L32p
32d2zjrz1
not modelled 81.7 25 Fold:Rubredoxin-like
Superfamily:Zn-binding ribosomal proteins
Family:Ribosomal protein L32p
33c1s24A_
not modelled 81.6 38 PDB header:electron transport
Chain: A: PDB Molecule:rubredoxin 2;
PDBTitle: rubredoxin domain ii from pseudomonas oleovorans
34d1s24a_
not modelled 81.6 38 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
35d2apob1
not modelled 81.5 45 Fold:Rubredoxin-like
Superfamily:Nop10-like SnoRNP
Family:Nucleolar RNA-binding protein Nop10-like
36d4rxna_
not modelled 81.3 32 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
37c2v3bB_
not modelled 81.2 35 PDB header:oxidoreductase
Chain: B: PDB Molecule:rubredoxin 2;
PDBTitle: crystal structure of the electron transfer complex2 rubredoxin - rubredoxin reductase from pseudomonas3 aeruginosa.
38d1iroa_
not modelled 81.0 32 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
39d1rb9a_
not modelled 80.8 32 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
40d2ey4e1
not modelled 80.4 40 Fold:Rubredoxin-like
Superfamily:Nop10-like SnoRNP
Family:Nucleolar RNA-binding protein Nop10-like
41c2gb5B_
not modelled 80.4 20 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
42d1h7va_
not modelled 80.3 30 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
43d2gnra1
not modelled 80.3 23 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:SSO2064-like
44d1qcva_
not modelled 80.3 19 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
45d1iu5a_
not modelled 79.8 36 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
46c3axtA_
not modelled 79.7 26 PDB header:transferase
Chain: A: PDB Molecule:probable n(2),n(2)-dimethylguanosine trna methyltransferase
PDBTitle: complex structure of trna methyltransferase trm1 from aquifex aeolicus2 with s-adenosyl-l-methionine
47d2dsxa1
not modelled 79.2 36 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
48c2k2dA_
not modelled 78.4 20 PDB header:metal binding protein
Chain: A: PDB Molecule:ring finger and chy zinc finger domain-
PDBTitle: solution nmr structure of c-terminal domain of human pirh2.2 northeast structural genomics consortium (nesg) target ht2c
49d1brfa_
not modelled 76.9 36 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
50c2ba1B_
not modelled 76.9 25 PDB header:rna binding protein
Chain: B: PDB Molecule:archaeal exosome rna binding protein csl4;
PDBTitle: archaeal exosome core
51d6rxna_
not modelled 76.5 32 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
52d2cona1
not modelled 73.9 35 Fold:Rubredoxin-like
Superfamily:NOB1 zinc finger-like
Family:NOB1 zinc finger-like
53c2qkdA_
not modelled 72.8 23 PDB header:signaling protein, cell cycle
Chain: A: PDB Molecule:zinc finger protein zpr1;
PDBTitle: crystal structure of tandem zpr1 domains
54c2nn6I_
not modelled 72.6 13 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
55d2rdva_
not modelled 72.4 48 Fold:Rubredoxin-like
Superfamily:Rubredoxin-like
Family:Rubredoxin
56d2fiya1
not modelled 70.3 30 Fold:FdhE-like
Superfamily:FdhE-like
Family:FdhE-like
57c2kn9A_
not modelled 70.2 42 PDB header:electron transport
Chain: A: PDB Molecule:rubredoxin;
PDBTitle: solution structure of zinc-substituted rubredoxin b (rv3250c) from2 mycobacterium tuberculosis. seattle structural genomics center for3 infectious disease target mytud.01635.a
58c2f9iD_
not modelled 69.1 22 PDB header:transferase
Chain: D: PDB Molecule:acetyl-coenzyme a carboxylase carboxyl
PDBTitle: crystal structure of the carboxyltransferase subunit of acc2 from staphylococcus aureus
59d2ct7a1
not modelled 66.0 28 Fold:RING/U-box
Superfamily:RING/U-box
Family:IBR domain
60d2qam01
not modelled 65.2 23 Fold:Rubredoxin-like
Superfamily:Zn-binding ribosomal proteins
Family:Ribosomal protein L32p
61c1u5kA_
not modelled 65.0 19 PDB header:recombination,replication
Chain: A: PDB Molecule:hypothetical protein;
PDBTitle: recombinational repair protein reco
62d2dkta1
not modelled 63.6 24 Fold:CHY zinc finger-like
Superfamily:CHY zinc finger-like
Family:CHY zinc finger
63d1pfva3
not modelled 62.7 30 Fold:Rubredoxin-like
Superfamily:Methionyl-tRNA synthetase (MetRS), Zn-domain
Family:Methionyl-tRNA synthetase (MetRS), Zn-domain
64c3ir9A_
not modelled 62.2 35 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:peptide chain release factor subunit 1;
PDBTitle: c-terminal domain of peptide chain release factor from2 methanosarcina mazei.
65c2ktvA_
not modelled 61.3 19 PDB header:translation
Chain: A: PDB Molecule:eukaryotic peptide chain release factor subunit 1;
PDBTitle: human erf1 c-domain, "open" conformer
66d1nuia2
not modelled 60.5 36 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:DNA primase zinc finger
67c2f9yB_
not modelled 59.8 32 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
68d2f9yb1
not modelled 59.8 32 Fold:ClpP/crotonase
Superfamily:ClpP/crotonase
Family:Biotin dependent carboxylase carboxyltransferase domain
69d1ltla_
not modelled 59.6 22 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:DNA replication initiator (cdc21/cdc54) N-terminal domain
70c2aklA_
not modelled 56.1 21 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
71c3f2cA_
not modelled 56.0 40 PDB header:transferase/dna
Chain: A: PDB Molecule:geobacillus kaustophilus dna polc;
PDBTitle: dna polymerase polc from geobacillus kaustophilus complex with dna,2 dgtp and mn
72d2nn6i1
not modelled 55.0 13 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
73c3cngC_
not modelled 54.5 29 PDB header:hydrolase
Chain: C: PDB Molecule:nudix hydrolase;
PDBTitle: crystal structure of nudix hydrolase from nitrosomonas europaea
74c1ltlE_
not modelled 54.1 22 PDB header:replication
Chain: E: PDB Molecule:dna replication initiator (cdc21/cdc54);
PDBTitle: the dodecamer structure of mcm from archaeal m.2 thermoautotrophicum
75c3bjiA_
not modelled 53.7 38 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
76d2akla2
not modelled 53.6 23 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:PhnA zinc-binding domain
77c1m2oA_
not modelled 53.0 13 PDB header:protein transport/signaling protein
Chain: A: PDB Molecule:protein transport protein sec23;
PDBTitle: crystal structure of the sec23-sar1 complex
78c2vl6C_
not modelled 51.4 30 PDB header:dna binding protein
Chain: C: PDB Molecule:minichromosome maintenance protein mcm;
PDBTitle: structural analysis of the sulfolobus solfataricus mcm2 protein n-terminal domain
79c1vddC_
not modelled 51.4 19 PDB header:recombination
Chain: C: PDB Molecule:recombination protein recr;
PDBTitle: crystal structure of recombinational repair protein recr
80d1pfta_
not modelled 51.2 25 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
81c2k5cA_
not modelled 48.1 56 PDB header:metal binding protein
Chain: A: PDB Molecule:uncharacterized protein pf0385;
PDBTitle: nmr structure for pf0385
82d1u5ka2
not modelled 48.0 19 Fold:ArfGap/RecO-like zinc finger
Superfamily:ArfGap/RecO-like zinc finger
Family:RecO C-terminal domain-like
83d1dl6a_
not modelled 47.9 29 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:Transcriptional factor domain
84d2dlqa2
not modelled 47.0 75 Fold:beta-beta-alpha zinc fingers
Superfamily:beta-beta-alpha zinc fingers
Family:Classic zinc finger, C2H2
85c3ky9B_
not modelled 47.0 38 PDB header:apoptosis
Chain: B: PDB Molecule:proto-oncogene vav;
PDBTitle: autoinhibited vav1
86d1ynjd1
not modelled 44.9 35 Fold:beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily:beta and beta-prime subunits of DNA dependent RNA-polymerase
Family:RNA-polymerase beta-prime
87c3gn5B_
not modelled 44.5 36 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)
88c3eswA_
not modelled 43.4 23 PDB header:hydrolase
Chain: A: PDB Molecule:peptide-n(4)-(n-acetyl-beta-glucosaminyl)asparagine
PDBTitle: complex of yeast pngase with glcnac2-iac.
89d2ctda2
not modelled 43.3 50 Fold:beta-beta-alpha zinc fingers
Superfamily:beta-beta-alpha zinc fingers
Family:Classic zinc finger, C2H2
90d1x6ma_
not modelled 42.6 28 Fold:Mss4-like
Superfamily:Mss4-like
Family:Glutathione-dependent formaldehyde-activating enzyme, Gfa
91c1ee8A_
not modelled 42.5 26 PDB header:dna binding protein
Chain: A: PDB Molecule:mutm (fpg) protein;
PDBTitle: crystal structure of mutm (fpg) protein from thermus thermophilus hb8
92c3eh2B_
not modelled 42.5 19 PDB header:protein transport
Chain: B: PDB Molecule:protein transport protein sec24c;
PDBTitle: crystal structure of the human copii-coat protein sec24c
93c1m2vB_
not modelled 42.2 20 PDB header:protein transport
Chain: B: PDB Molecule:protein transport protein sec24;
PDBTitle: crystal structure of the yeast sec23/24 heterodimer
94c2owoA_
not modelled 41.0 44 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
95c3k7aM_
not modelled 40.3 29 PDB header:transcription
Chain: M: PDB Molecule:transcription initiation factor iib;
PDBTitle: crystal structure of an rna polymerase ii-tfiib complex
96c3h0gN_
not modelled 40.0 21 PDB header:transcription
Chain: N: PDB Molecule:dna-directed rna polymerase ii subunit rpb2;
PDBTitle: rna polymerase ii from schizosaccharomyces pombe
97c2ysaA_
not modelled 39.7 21 PDB header:metal binding protein
Chain: A: PDB Molecule:retinoblastoma-binding protein 6;
PDBTitle: solution structure of the zinc finger cchc domain from the2 human retinoblastoma-binding protein 6 (retinoblastoma-3 binding q protein 1, rbq-1)
98c3cw2M_
not modelled 39.2 22 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 .
99c1pd0A_
not modelled 39.2 20 PDB header:transport protein
Chain: A: PDB Molecule:protein transport protein sec24;
PDBTitle: crystal structure of the copii coat subunit, sec24,2 complexed with a peptide from the snare protein sed53 (yeast syntaxin-5)
100d1vdda_
not modelled 39.1 23 Fold:Recombination protein RecR
Superfamily:Recombination protein RecR
Family:Recombination protein RecR
101c2opfA_
not modelled 38.5 33 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
102c3eg9B_
not modelled 38.4 16 PDB header:protein transport
Chain: B: PDB Molecule:sec24 related gene family, member d;
PDBTitle: crystal structure of the mammalian copii-coat protein2 sec23/24 bound to the transport signal sequence of membrin
103c2yqqA_
not modelled 38.1 29 PDB header:protein binding
Chain: A: PDB Molecule:zinc finger hit domain-containing protein 3;
PDBTitle: solution structure of the zf-hit domain in zinc finger hit2 domain-containing protein 3 (trip-3)
104d1j6wa_
not modelled 38.1 57 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:Autoinducer-2 production protein LuxS
105c3h7hA_
not modelled 38.1 19 PDB header:transcription
Chain: A: PDB Molecule:transcription elongation factor spt4;
PDBTitle: crystal structure of the human transcription elongation factor dsif,2 hspt4/hspt5 (176-273)
106c2pmzB_
not modelled 38.0 28 PDB header:translation, transferase
Chain: B: PDB Molecule:dna-directed rna polymerase subunit b;
PDBTitle: archaeal rna polymerase from sulfolobus solfataricus
107c2ja6L_
not modelled 37.7 21 PDB header:transferase
Chain: L: PDB Molecule:dna-directed rna polymerases i, ii, and iii 7.7
PDBTitle: cpd lesion containing rna polymerase ii elongation complex2 b
108c2bx9J_
not modelled 37.3 35 PDB header:transcription regulation
Chain: J: PDB Molecule:tryptophan rna-binding attenuator protein-inhibitory
PDBTitle: crystal structure of b.subtilis anti-trap protein, an2 antagonist of trap-rna interactions
109c3na7A_
not modelled 37.3 20 PDB header:gene regulation, chaperone
Chain: A: PDB Molecule:hp0958;
PDBTitle: 2.2 angstrom structure of the hp0958 protein from helicobacter pylori2 ccug 17874
110c3h0gL_
not modelled 36.8 21 PDB header:transcription
Chain: L: PDB Molecule:dna-directed rna polymerases i, ii, and iii
PDBTitle: rna polymerase ii from schizosaccharomyces pombe
111d1x3za1
not modelled 36.7 22 Fold:Cysteine proteinases
Superfamily:Cysteine proteinases
Family:Transglutaminase core
112c1nnjA_
not modelled 36.6 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
113c2f5qA_
not modelled 35.9 32 PDB header:hydrolase/dna
Chain: A: PDB Molecule:formamidopyrimidine-dna glycosidase;
PDBTitle: catalytically inactive (e3q) mutm crosslinked to oxog:c2 containing dna cc2
114c3pkiF_
not modelled 35.5 28 PDB header:hydrolase
Chain: F: PDB Molecule:nad-dependent deacetylase sirtuin-6;
PDBTitle: human sirt6 crystal structure in complex with adp ribose
115d1j6xa_
not modelled 35.3 43 Fold:LuxS/MPP-like metallohydrolase
Superfamily:LuxS/MPP-like metallohydrolase
Family:Autoinducer-2 production protein LuxS
116c1v9pB_
not modelled 35.3 56 PDB header:ligase
Chain: B: PDB Molecule:dna ligase;
PDBTitle: crystal structure of nad+-dependent dna ligase
117d2dula1
not modelled 35.1 17 Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:TRM1-like
118d1srka_
not modelled 35.0 33 Fold:beta-beta-alpha zinc fingers
Superfamily:beta-beta-alpha zinc fingers
Family:Classic zinc finger, C2H2
119c3pfqA_
not modelled 35.0 29 PDB header:transferase
Chain: A: PDB Molecule:protein kinase c beta type;
PDBTitle: crystal structure and allosteric activation of protein kinase c beta2 ii
120c3f9vA_
not modelled 34.9 30 PDB header:hydrolase
Chain: A: PDB Molecule:minichromosome maintenance protein mcm;
PDBTitle: crystal structure of a near full-length archaeal mcm: functional2 insights for an aaa+ hexameric helicase

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
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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