Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP39452
DateThu Jan 5 12:00:51 GMT 2012
Unique Job IDca69fe18963e570d

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1pemA_
Top template information
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase 2 alpha
PDBTitle: ribonucleotide reductase protein r1e from salmonella2 typhimurium
Confidence and coverage
Confidence:100.0% Coverage: 96%
682 residues ( 96% 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  MATTTAECLTQETMDYHALNAMLNLYDSAGRIQFDKDRQAVDAFIATHVRPNSVTFSSQQ
Secondary structure 
SS confidence 
Disorder  ?
?
??
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  QRLNWLVNEGYYDESVLNRYSRDFVITLFTHAHTSGFRFQTFLGAWKFYTSYTLKTFDGK
Secondary structure 
SS confidence 
Disorder 
?
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  RYLEDFADRVTMVALTLAQGDETLALQLTDEMLSGRFQPATPTFLNCGKQQRGELVSCFL
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  LRIEDNMESIGRAVNSALQLSKRGGGVAFLLSNLREAGAPIKRIENQSSGVIPVMKMLED
Secondary structure 
SS confidence 
Disorder 
??????
?
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  AFSYANQLGARQGAGAVYLHAHHPDILRFLDTKRENADEKIRIKTLSLGVVIPDITFHLA
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  KENAQMALFSPYDVERVYGKPFADVAISQHYDELVADERIRKKYLNARDFFQRLAEIQFE
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  SGYPYIMYEDTVNRANPIAGRINMSNLCSEILQVNSASEYDENLDYTRTGHDISCNLGSL
Secondary structure 
SS confidence 
Disorder 
?
?
?
?
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  NIAHTMDSPDFARTVETAVRGLTAVSDMSHIRSVPSIEAGNAASHAIGLGQMNLHGYLAR
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  EGIAYGSPEALDFTNLYFYAITWHALRTSMLLARERGETFAGFKQSRYASGEYFSQYLQG
Secondary structure 
SS confidence 
Disorder 
??
?
???
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  NWQPKTAKVGELFTRSGITLPTREMWAQLRDDVMRYGIYNQNLQAVPPTGSISYINHATS
Secondary structure 
SS confidence 
Disorder 
??
??
?
?
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  SIHPIVAKVEIRKEGKTGRVYYPAPFMTNENLALYQDAYEIGAEKIIDTYAEATRHVDQG
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........670.........680.........690.........700.........710....
Sequence  LSLTLFFPDTATTRDINKAQIYAWRKGIKTLYYIRLRQMALEGTEIEGCVSCAL
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 1pem chain A

3D model

Region: 13 - 699
Aligned: 682
Modelled: 687
Confidence: 100.0%
Identity: 90%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase 2 alpha
PDBTitle: ribonucleotide reductase protein r1e from salmonella2 typhimurium

Phyre2

PDB 3r1r chain B

3D model

Region: 1 - 698
Aligned: 659
Modelled: 664
Confidence: 100.0%
Identity: 23%
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 2wgh chain A

3D model

Region: 19 - 697
Aligned: 620
Modelled: 630
Confidence: 100.0%
Identity: 26%
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 3hnf chain A

3D model

Region: 1 - 697
Aligned: 625
Modelled: 653
Confidence: 100.0%
Identity: 28%
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: 51 - 697
Aligned: 606
Modelled: 617
Confidence: 100.0%
Identity: 27%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large chain
PDBTitle: structures of yeast ribonucleotide reductase i

Phyre2

PDB 1xje chain A

3D model

Region: 87 - 698
Aligned: 542
Modelled: 551
Confidence: 100.0%
Identity: 27%
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 1rlr chain A domain 2

3D model

Region: 175 - 714
Aligned: 514
Modelled: 534
Confidence: 100.0%
Identity: 26%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: R1 subunit of ribonucleotide reductase, C-terminal domain

Phyre2

PDB 1peq chain A domain 2

3D model

Region: 175 - 699
Aligned: 512
Modelled: 525
Confidence: 100.0%
Identity: 91%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: R1 subunit of ribonucleotide reductase, C-terminal domain

Phyre2

PDB 1l1l chain A

3D model

Region: 71 - 705
Aligned: 523
Modelled: 540
Confidence: 100.0%
Identity: 19%
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 1

3D model

Region: 13 - 174
Aligned: 162
Modelled: 162
Confidence: 100.0%
Identity: 85%
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 1rlr chain A domain 1

3D model

Region: 1 - 174
Aligned: 155
Modelled: 156
Confidence: 100.0%
Identity: 14%
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 1hk8 chain A

3D model

Region: 349 - 712
Aligned: 256
Modelled: 285
Confidence: 95.0%
Identity: 17%
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: 349 - 712
Aligned: 256
Modelled: 285
Confidence: 95.0%
Identity: 17%
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 1h16 chain A

3D model

Region: 348 - 504
Aligned: 140
Modelled: 140
Confidence: 76.3%
Identity: 14%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: PFL-like

Phyre2

PDB 3pg6 chain D

3D model

Region: 654 - 691
Aligned: 36
Modelled: 38
Confidence: 53.3%
Identity: 25%
PDB header:ligase
Chain: D: PDB Molecule:e3 ubiquitin-protein ligase dtx3l;
PDBTitle: the carboxyl terminal domain of human deltex 3-like

Phyre2

PDB 1qhm chain A

3D model

Region: 348 - 477
Aligned: 113
Modelled: 113
Confidence: 32.3%
Identity: 14%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: PFL-like

Phyre2

PDB 2okq chain A domain 1

3D model

Region: 174 - 209
Aligned: 36
Modelled: 36
Confidence: 29.1%
Identity: 19%
Fold: Ferredoxin-like
Superfamily: Dimeric alpha+beta barrel
Family: YbaA-like

Phyre2

PDB 1geq chain A

3D model

Region: 191 - 302
Aligned: 103
Modelled: 112
Confidence: 27.1%
Identity: 13%
Fold: TIM beta/alpha-barrel
Superfamily: Ribulose-phoshate binding barrel
Family: Tryptophan biosynthesis enzymes

Phyre2

PDB 1h3o chain B

3D model

Region: 487 - 518
Aligned: 32
Modelled: 32
Confidence: 22.9%
Identity: 13%
Fold: Histone-fold
Superfamily: Histone-fold
Family: TBP-associated factors, TAFs

Phyre2

PDB 2ccq chain A domain 1

3D model

Region: 427 - 483
Aligned: 57
Modelled: 57
Confidence: 22.4%
Identity: 16%
Fold: PUG domain-like
Superfamily: PUG domain-like
Family: PUG domain

Phyre2
1
c1pemA_
2
c3r1rB_
3
c2wghA_
4
c3hnfA_
5
c2cvuA_
6
c1xjeA_
7
d1rlra2
8
d1peqa2
9
d1l1la_
10
d1peqa1
11
d1rlra1
12
d1hk8a_
13
c1hk8A_
14
d1h16a_
15
c3pg6D_
16
d1qhma_
17
d2okqa1
18
d1geqa_
19
d1h3ob_
20
d2ccqa1
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1pemA_
100.0 90 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase 2 alpha
PDBTitle: ribonucleotide reductase protein r1e from salmonella2 typhimurium
2c3r1rB_
100.0 23 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
3c2wghA_
100.0 26 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large
PDBTitle: human ribonucleotide reductase r1 subunit (rrm1) in complex2 with datp and mg.
4c3hnfA_
100.0 28 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_
100.0 27 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large chain
PDBTitle: structures of yeast ribonucleotide reductase i
6c1xjeA_
100.0 27 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
7d1rlra2
100.0 26 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:R1 subunit of ribonucleotide reductase, C-terminal domain
8d1peqa2
100.0 91 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:R1 subunit of ribonucleotide reductase, C-terminal domain
9d1l1la_
100.0 19 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:B12-dependent (class II) ribonucleotide reductase
10d1peqa1
100.0 85 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
11d1rlra1
100.0 14 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
12d1hk8a_
95.0 17 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:Class III anaerobic ribonucleotide reductase NRDD subunit
13c1hk8A_
95.0 17 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
14d1h16a_
76.3 14 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
15c3pg6D_
53.3 25 PDB header:ligase
Chain: D: PDB Molecule:e3 ubiquitin-protein ligase dtx3l;
PDBTitle: the carboxyl terminal domain of human deltex 3-like
16d1qhma_
32.3 14 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
17d2okqa1
29.1 19 Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:YbaA-like
18d1geqa_
27.1 13 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
19d1h3ob_
22.9 13 Fold:Histone-fold
Superfamily:Histone-fold
Family:TBP-associated factors, TAFs
20d2ccqa1
22.4 16 Fold:PUG domain-like
Superfamily:PUG domain-like
Family:PUG domain
21c2okqB_
not modelled 20.1 19 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:hypothetical protein ybaa;
PDBTitle: crystal structure of unknown conserved ybaa protein from2 shigella flexneri
22d1jlia_
not modelled 15.7 22 Fold:4-helical cytokines
Superfamily:4-helical cytokines
Family:Short-chain cytokines
23d1msza_
not modelled 13.8 17 Fold:IF3-like
Superfamily:R3H domain
Family:R3H domain
24c1mszA_
not modelled 13.8 17 PDB header:dna binding protein
Chain: A: PDB Molecule:dna-binding protein smubp-2;
PDBTitle: solution structure of the r3h domain from human smubp-2
25d2b4va2
not modelled 12.7 44 Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:RNA editing terminal uridyl transferase 2, RET2, catalytic domain
26c3pe0B_
not modelled 12.7 24 PDB header:structural protein
Chain: B: PDB Molecule:plectin;
PDBTitle: structure of the central region of the plakin domain of plectin
27d1v93a_
not modelled 12.1 16 Fold:TIM beta/alpha-barrel
Superfamily:FAD-linked oxidoreductase
Family:Methylenetetrahydrofolate reductase
28c1pgjA_
not modelled 12.0 44 PDB header:oxidoreductase
Chain: A: PDB Molecule:6-phosphogluconate dehydrogenase;
PDBTitle: x-ray structure of 6-phosphogluconate dehydrogenase from the protozoan2 parasite t. brucei
29d1v74b_
not modelled 11.6 18 Fold:Four-helical up-and-down bundle
Superfamily:Colicin D immunity protein
Family:Colicin D immunity protein
30d1vkna2
not modelled 10.9 14 Fold:FwdE/GAPDH domain-like
Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family:GAPDH-like
31c2iz1C_
not modelled 10.9 28 PDB header:oxidoreductase
Chain: C: PDB Molecule:6-phosphogluconate dehydrogenase, decarboxylating;
PDBTitle: 6pdh complexed with pex inhibitor synchrotron data
32d1ic8a2
not modelled 10.8 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:POU-specific domain
33c3rcqA_
not modelled 10.6 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:aspartyl/asparaginyl beta-hydroxylase;
PDBTitle: crystal structure of human aspartate beta-hydroxylase isoform a
34c2v3sB_
not modelled 10.5 14 PDB header:transferase
Chain: B: PDB Molecule:serine/threonine-protein kinase osr1;
PDBTitle: structural insights into the recognition of substrates and2 activators by the osr1 kinase
35d2uyoa1
not modelled 10.3 14 Fold:S-adenosyl-L-methionine-dependent methyltransferases
Superfamily:S-adenosyl-L-methionine-dependent methyltransferases
Family:ML2640-like
36d1vmha_
not modelled 10.2 10 Fold:YjbQ-like
Superfamily:YjbQ-like
Family:YjbQ-like
37c2f3oB_
not modelled 10.1 18 PDB header:unknown function
Chain: B: PDB Molecule:pyruvate formate-lyase 2;
PDBTitle: crystal structure of a glycyl radical enzyme from archaeoglobus2 fulgidus
38d1vmfa_
not modelled 9.7 10 Fold:YjbQ-like
Superfamily:YjbQ-like
Family:YjbQ-like
39c2p4qA_
not modelled 9.5 44 PDB header:oxidoreductase
Chain: A: PDB Molecule:6-phosphogluconate dehydrogenase, decarboxylating 1;
PDBTitle: crystal structure analysis of gnd1 in saccharomyces cerevisiae
40c3fwnB_
not modelled 9.2 28 PDB header:oxidoreductase
Chain: B: PDB Molecule:6-phosphogluconate dehydrogenase, decarboxylating;
PDBTitle: dimeric 6-phosphogluconate dehydrogenase complexed with 6-2 phosphogluconate and 2'-monophosphoadenosine-5'-diphosphate
41d1vmja_
not modelled 9.2 20 Fold:YjbQ-like
Superfamily:YjbQ-like
Family:YjbQ-like
42d1j09a2
not modelled 8.9 15 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
43d2d5ua1
not modelled 8.6 16 Fold:PUG domain-like
Superfamily:PUG domain-like
Family:PUG domain
44c2p6hB_
not modelled 8.2 13 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:hypothetical protein;
PDBTitle: crystal structure of hypothetical protein ape1520 from aeropyrum2 pernix k1
45d1r9da_
not modelled 7.7 17 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
46d1gv2a2
not modelled 7.7 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Myb/SANT domain
47c1pgqA_
not modelled 7.6 39 PDB header:oxidoreductase (choh(d)-nadp+(a))
Chain: A: PDB Molecule:6-phosphogluconate dehydrogenase;
PDBTitle: crystallographic study of coenzyme, coenzyme analogue and substrate2 binding in 6-phosphogluconate dehydrogenase: implications for nadp3 specificity and the enzyme mechanism
48c1idzA_
not modelled 7.3 21 PDB header:dna-binding protein
Chain: A: PDB Molecule:mouse c-myb dna-binding domain repeat 3;
PDBTitle: structure of myb transforming protein, nmr, 20 structures
49c2xrgA_
not modelled 7.2 13 PDB header:hydrolase
Chain: A: PDB Molecule:ectonucleotide pyrophosphatase/phosphodiesterase family
PDBTitle: crystal structure of autotaxin (enpp2) in complex with the2 ha155 boronic acid inhibitor
50d1wiga2
not modelled 7.2 33 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:LIM domain
51d2d0ob1
not modelled 7.1 16 Fold:Anticodon-binding domain-like
Superfamily:B12-dependent dehydatase associated subunit
Family:Dehydratase-reactivating factor beta subunit
52c2p6cB_
not modelled 6.9 10 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:aq_2013 protein;
PDBTitle: crystal structure of hypothetical protein aq_2013 from aquifex2 aeolicus vf5.
53c3ng3A_
not modelled 6.9 31 PDB header:lyase
Chain: A: PDB Molecule:deoxyribose-phosphate aldolase;
PDBTitle: crystal structure of deoxyribose phosphate aldolase from mycobacterium2 avium 104 in a schiff base with an unknown aldehyde
54d2csba2
not modelled 6.8 42 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:Topoisomerase V repeat domain
55c3hm6X_
not modelled 6.8 16 PDB header:signaling protein
Chain: X: PDB Molecule:plexin-b1;
PDBTitle: crystal structure of the cytoplasmic domain of human plexin b1
56d2b3wa1
not modelled 6.6 20 Fold:YbiA-like
Superfamily:YbiA-like
Family:YbiA-like
57c2qlwA_
not modelled 6.4 27 PDB header:isomerase
Chain: A: PDB Molecule:rhau;
PDBTitle: crystal structure of rhamnose mutarotase rhau of rhizobium2 leguminosarum
58c2qlxA_
not modelled 6.4 27 PDB header:isomerase
Chain: A: PDB Molecule:l-rhamnose mutarotase;
PDBTitle: crystal structure of rhamnose mutarotase rhau of rhizobium2 leguminosarum in complex with l-rhamnose
59d1vpha_
not modelled 6.3 16 Fold:YjbQ-like
Superfamily:YjbQ-like
Family:YjbQ-like
60c2c1fA_
not modelled 6.3 24 PDB header:hydrolase
Chain: A: PDB Molecule:bifunctional endo-1,4-beta-xylanase a;
PDBTitle: the structure of the family 11 xylanase from neocallimastix2 patriciarum
61d2g5ca2
not modelled 6.2 28 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
62c3dzbA_
not modelled 6.0 32 PDB header:biosynthetic protein
Chain: A: PDB Molecule:prephenate dehydrogenase;
PDBTitle: crystal structure of prephenate dehydrogenase from streptococcus2 thermophilus
63d1f0ya2
not modelled 6.0 33 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
64c3a9lB_
not modelled 6.0 15 PDB header:hydrolase
Chain: B: PDB Molecule:poly-gamma-glutamate hydrolase;
PDBTitle: structure of bacteriophage poly-gamma-glutamate hydrolase
65c2is9A_
not modelled 5.9 24 PDB header:transcription
Chain: A: PDB Molecule:defective in cullin neddylation protein 1;
PDBTitle: structure of yeast dcn-1
66d1mbja_
not modelled 5.8 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Myb/SANT domain
67c1mbjA_
not modelled 5.8 18 PDB header:dna binding protein
Chain: A: PDB Molecule:myb proto-oncogene protein;
PDBTitle: mouse c-myb dna-binding domain repeat 3
68c1obfO_
not modelled 5.8 19 PDB header:glycolytic pathway
Chain: O: PDB Molecule:glyceraldehyde 3-phosphate dehydrogenase;
PDBTitle: the crystal structure of glyceraldehyde 3-phosphate2 dehydrogenase from alcaligenes xylosoxidans at 1.73 resolution.
69d1k3ta2
not modelled 5.7 22 Fold:FwdE/GAPDH domain-like
Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family:GAPDH-like
70d1jfla1
not modelled 5.7 32 Fold:ATC-like
Superfamily:Aspartate/glutamate racemase
Family:Aspartate/glutamate racemase
71d1h4ga_
not modelled 5.6 24 Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Xylanase/endoglucanase 11/12
72d1f5ja_
not modelled 5.6 29 Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Xylanase/endoglucanase 11/12
73c2jr7A_
not modelled 5.6 26 PDB header:metal binding protein
Chain: A: PDB Molecule:dph3 homolog;
PDBTitle: solution structure of human desr1
74c3ivuB_
not modelled 5.6 11 PDB header:transferase
Chain: B: PDB Molecule:homocitrate synthase, mitochondrial;
PDBTitle: homocitrate synthase lys4 bound to 2-og
75c3iymA_
not modelled 5.6 20 PDB header:virus
Chain: A: PDB Molecule:capsid protein;
PDBTitle: backbone trace of the capsid protein dimer of a fungal partitivirus2 from electron cryomicroscopy and homology modeling
76d1x8da1
not modelled 5.5 27 Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:YiiL-like
77d1te1b_
not modelled 5.4 29 Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Xylanase/endoglucanase 11/12
78d1m4wa_
not modelled 5.4 29 Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Xylanase/endoglucanase 11/12
79d1wgea1
not modelled 5.4 23 Fold:Rubredoxin-like
Superfamily:CSL zinc finger
Family:CSL zinc finger
80d2awia2
not modelled 5.4 10 Fold:alpha-alpha superhelix
Superfamily:TPR-like
Family:PrgX C-terminal domain-like
81d1xyna_
not modelled 5.4 24 Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Xylanase/endoglucanase 11/12
82c2dcjA_
not modelled 5.4 24 PDB header:hydrolase
Chain: A: PDB Molecule:xylanase j;
PDBTitle: a two-domain structure of alkaliphilic xynj from bacillus sp. 41m-1
83c2g5cD_
not modelled 5.2 26 PDB header:oxidoreductase
Chain: D: PDB Molecule:prephenate dehydrogenase;
PDBTitle: crystal structure of prephenate dehydrogenase from aquifex aeolicus
84c2kzuA_
not modelled 5.2 31 PDB header:apoptosis
Chain: A: PDB Molecule:death-associated protein 6;
PDBTitle: daxx helical bundle (dhb) domain / rassf1c complex
85d1t6gc_
not modelled 5.1 18 Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Xylanase/endoglucanase 11/12
86d1xi8a3
not modelled 5.1 28 Fold:Molybdenum cofactor biosynthesis proteins
Superfamily:Molybdenum cofactor biosynthesis proteins
Family:MoeA central domain-like
87d1at3a_
not modelled 5.1 40 Fold:Herpes virus serine proteinase, assemblin
Superfamily:Herpes virus serine proteinase, assemblin
Family:Herpes virus serine proteinase, assemblin
88d1igoa_
not modelled 5.1 18 Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Xylanase/endoglucanase 11/12
89c2p6uA_
not modelled 5.1 28 PDB header:dna binding protein
Chain: A: PDB Molecule:afuhel308 helicase;
PDBTitle: apo structure of the hel308 superfamily 2 helicase
90c2pv7B_
not modelled 5.0 28 PDB header:isomerase, oxidoreductase
Chain: B: PDB Molecule:t-protein [includes: chorismate mutase (ec 5.4.99.5) (cm)
PDBTitle: crystal structure of chorismate mutase / prephenate dehydrogenase2 (tyra) (1574749) from haemophilus influenzae rd at 2.00 a resolution

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