Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP00452
DateThu Jan 5 10:56:38 GMT 2012
Unique Job IDd37d29b94415048c

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3r1rB_
Top template information
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
Confidence and coverage
Confidence:100.0% Coverage: 96%
733 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  MNQNLLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHE
Secondary structure 
SS confidence 
Disorder  ????
?
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  TIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLL
Secondary structure 
SS confidence 
Disorder 
???
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  EDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACL
Secondary structure 
SS confidence 
Disorder 
??
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  FSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINAT
Secondary structure 
SS confidence 
Disorder 
??
?
??
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  SSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGG
Secondary structure 
SS confidence 
Disorder 
????
?
?
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  AATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSD
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  VPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHC
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  NTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEE
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........490.........500.........510.........520.........530.........540
Sequence  LAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLT
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........550.........560.........570.........580.........590.........600
Sequence  HKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWE
Secondary structure 
SS confidence 
Disorder 
?
?
?
Disorder confidence 
 
   .........610.........620.........630.........640.........650.........660
Sequence  ALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYE
Secondary structure 
SS confidence 
Disorder 
?
?
??????
Disorder confidence 
 
   .........670.........680.........690.........700.........710.........720
Sequence  HLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLT
Secondary structure 
SS confidence 
Disorder 
?????
Disorder confidence 
 
   .........730.........740.........750.........760.
Sequence  AYKFGVKTLYYQNTRDGAEDAQDDLVPSIQDDGCESGACKI
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 3r1r chain B

3D model

Region: 5 - 737
Aligned: 733
Modelled: 733
Confidence: 100.0%
Identity: 100%
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: 19 - 735
Aligned: 669
Modelled: 700
Confidence: 100.0%
Identity: 30%
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 2wgh chain A

3D model

Region: 80 - 735
Aligned: 622
Modelled: 643
Confidence: 100.0%
Identity: 30%
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 1pem chain A

3D model

Region: 81 - 736
Aligned: 632
Modelled: 656
Confidence: 100.0%
Identity: 22%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase 2 alpha
PDBTitle: ribonucleotide reductase protein r1e from salmonella2 typhimurium

Phyre2

PDB 2cvu chain A

3D model

Region: 92 - 735
Aligned: 609
Modelled: 628
Confidence: 100.0%
Identity: 29%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large chain
PDBTitle: structures of yeast ribonucleotide reductase i

Phyre2

PDB 1rlr chain A domain 2

3D model

Region: 222 - 743
Aligned: 522
Modelled: 522
Confidence: 100.0%
Identity: 99%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: R1 subunit of ribonucleotide reductase, C-terminal domain

Phyre2

PDB 1xje chain A

3D model

Region: 130 - 736
Aligned: 546
Modelled: 568
Confidence: 100.0%
Identity: 20%
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 1peq chain A domain 2

3D model

Region: 222 - 736
Aligned: 491
Modelled: 512
Confidence: 100.0%
Identity: 25%
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: 115 - 730
Aligned: 515
Modelled: 526
Confidence: 100.0%
Identity: 15%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: B12-dependent (class II) ribonucleotide reductase

Phyre2

PDB 1rlr chain A domain 1

3D model

Region: 10 - 221
Aligned: 212
Modelled: 212
Confidence: 100.0%
Identity: 100%
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 1peq chain A domain 1

3D model

Region: 74 - 220
Aligned: 139
Modelled: 142
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: 397 - 557
Aligned: 140
Modelled: 161
Confidence: 95.3%
Identity: 13%
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: 397 - 557
Aligned: 140
Modelled: 161
Confidence: 95.3%
Identity: 13%
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: 396 - 583
Aligned: 161
Modelled: 188
Confidence: 86.4%
Identity: 19%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: PFL-like

Phyre2

PDB 1qhm chain A

3D model

Region: 396 - 527
Aligned: 116
Modelled: 132
Confidence: 43.8%
Identity: 17%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: PFL-like

Phyre2

PDB 2f3o chain B

3D model

Region: 397 - 583
Aligned: 166
Modelled: 187
Confidence: 43.3%
Identity: 19%
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 1r9d chain A

3D model

Region: 397 - 583
Aligned: 166
Modelled: 187
Confidence: 42.8%
Identity: 16%
Fold: PFL-like glycyl radical enzymes
Superfamily: PFL-like glycyl radical enzymes
Family: PFL-like

Phyre2

PDB 1h3o chain B

3D model

Region: 533 - 564
Aligned: 32
Modelled: 32
Confidence: 34.1%
Identity: 13%
Fold: Histone-fold
Superfamily: Histone-fold
Family: TBP-associated factors, TAFs

Phyre2

PDB 2okq chain A domain 1

3D model

Region: 221 - 256
Aligned: 36
Modelled: 36
Confidence: 33.0%
Identity: 8%
Fold: Ferredoxin-like
Superfamily: Dimeric alpha+beta barrel
Family: YbaA-like

Phyre2

PDB 1vjf chain A

3D model

Region: 520 - 641
Aligned: 99
Modelled: 122
Confidence: 31.5%
Identity: 18%
Fold: YbaK/ProRS associated domain
Superfamily: YbaK/ProRS associated domain
Family: YbaK/ProRS associated domain

Phyre2
1
c3r1rB_
2
c3hnfA_
3
c2wghA_
4
c1pemA_
5
c2cvuA_
6
d1rlra2
7
c1xjeA_
8
d1peqa2
9
d1l1la_
10
d1rlra1
11
d1peqa1
12
d1hk8a_
13
c1hk8A_
14
d1h16a_
15
d1qhma_
16
c2f3oB_
17
d1r9da_
18
d1h3ob_
19
d2okqa1
20
d1vjfa_
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
91
92
93
94
95
96
97
98
99



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3r1rB_
100.0 100 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
2c3hnfA_
100.0 30 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
3c2wghA_
100.0 30 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large
PDBTitle: human ribonucleotide reductase r1 subunit (rrm1) in complex2 with datp and mg.
4c1pemA_
100.0 22 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase 2 alpha
PDBTitle: ribonucleotide reductase protein r1e from salmonella2 typhimurium
5c2cvuA_
100.0 29 PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large chain
PDBTitle: structures of yeast ribonucleotide reductase i
6d1rlra2
100.0 99 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:R1 subunit of ribonucleotide reductase, C-terminal domain
7c1xjeA_
100.0 20 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
8d1peqa2
100.0 25 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:R1 subunit of ribonucleotide reductase, C-terminal domain
9d1l1la_
100.0 15 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:B12-dependent (class II) ribonucleotide reductase
10d1rlra1
100.0 100 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
11d1peqa1
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_
95.3 13 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:Class III anaerobic ribonucleotide reductase NRDD subunit
13c1hk8A_
95.3 13 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_
86.4 19 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
15d1qhma_
43.8 17 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
16c2f3oB_
43.3 19 PDB header:unknown function
Chain: B: PDB Molecule:pyruvate formate-lyase 2;
PDBTitle: crystal structure of a glycyl radical enzyme from archaeoglobus2 fulgidus
17d1r9da_
42.8 16 Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
18d1h3ob_
34.1 13 Fold:Histone-fold
Superfamily:Histone-fold
Family:TBP-associated factors, TAFs
19d2okqa1
33.0 8 Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:YbaA-like
20d1vjfa_
31.5 18 Fold:YbaK/ProRS associated domain
Superfamily:YbaK/ProRS associated domain
Family:YbaK/ProRS associated domain
21c2okqB_
not modelled 22.8 8 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:hypothetical protein ybaa;
PDBTitle: crystal structure of unknown conserved ybaa protein from2 shigella flexneri
22c2bjgB_
not modelled 22.6 12 PDB header:hydrolase
Chain: B: PDB Molecule:choloylglycine hydrolase;
PDBTitle: crystal structure of conjugated bile acid hydrolase from2 clostridium perfringens in complex with reaction products3 taurine and deoxycholate
23c2hezB_
not modelled 20.8 14 PDB header:hydrolase
Chain: B: PDB Molecule:bile salt hydrolase;
PDBTitle: bifidobacterium longum bile salt hydrolase
24d2pvaa_
not modelled 19.7 12 Fold:Ntn hydrolase-like
Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family:Penicillin V acylase
25d1j09a2
not modelled 19.2 14 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
26d2ccqa1
not modelled 18.5 16 Fold:PUG domain-like
Superfamily:PUG domain-like
Family:PUG domain
27c1pgjA_
not modelled 14.7 39 PDB header:oxidoreductase
Chain: A: PDB Molecule:6-phosphogluconate dehydrogenase;
PDBTitle: x-ray structure of 6-phosphogluconate dehydrogenase from the protozoan2 parasite t. brucei
28c3pg6D_
not modelled 14.5 15 PDB header:ligase
Chain: D: PDB Molecule:e3 ubiquitin-protein ligase dtx3l;
PDBTitle: the carboxyl terminal domain of human deltex 3-like
29d2b4va2
not modelled 13.7 44 Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:RNA editing terminal uridyl transferase 2, RET2, catalytic domain
30c2iz1C_
not modelled 13.7 28 PDB header:oxidoreductase
Chain: C: PDB Molecule:6-phosphogluconate dehydrogenase, decarboxylating;
PDBTitle: 6pdh complexed with pex inhibitor synchrotron data
31d1vmha_
not modelled 12.1 13 Fold:YjbQ-like
Superfamily:YjbQ-like
Family:YjbQ-like
32d1vmfa_
not modelled 12.1 16 Fold:YjbQ-like
Superfamily:YjbQ-like
Family:YjbQ-like
33d1ywsa1
not modelled 12.1 21 Fold:Rubredoxin-like
Superfamily:CSL zinc finger
Family:CSL zinc finger
34d1mska_
not modelled 12.1 20 Fold:Methionine synthase activation domain-like
Superfamily:Methionine synthase activation domain-like
Family:Methionine synthase SAM-binding domain
35c2p4qA_
not modelled 12.0 33 PDB header:oxidoreductase
Chain: A: PDB Molecule:6-phosphogluconate dehydrogenase, decarboxylating 1;
PDBTitle: crystal structure analysis of gnd1 in saccharomyces cerevisiae
36c2jr7A_
not modelled 11.6 21 PDB header:metal binding protein
Chain: A: PDB Molecule:dph3 homolog;
PDBTitle: solution structure of human desr1
37d1vmja_
not modelled 11.5 26 Fold:YjbQ-like
Superfamily:YjbQ-like
Family:YjbQ-like
38d1wgea1
not modelled 11.2 21 Fold:Rubredoxin-like
Superfamily:CSL zinc finger
Family:CSL zinc finger
39d1avca2
not modelled 10.9 14 Fold:Annexin
Superfamily:Annexin
Family:Annexin
40d1vkia_
not modelled 10.5 13 Fold:YbaK/ProRS associated domain
Superfamily:YbaK/ProRS associated domain
Family:YbaK/ProRS associated domain
41c2p6hB_
not modelled 10.3 26 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:hypothetical protein;
PDBTitle: crystal structure of hypothetical protein ape1520 from aeropyrum2 pernix k1
42c2xrgA_
not modelled 10.3 11 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
43c2oqcB_
not modelled 10.3 10 PDB header:hydrolase
Chain: B: PDB Molecule:penicillin v acylase;
PDBTitle: crystal structure of penicillin v acylase from bacillus subtilis
44d1xn7a_
not modelled 10.3 64 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Hypothetical protein YhgG
45d2d0ob1
not modelled 9.6 10 Fold:Anticodon-binding domain-like
Superfamily:B12-dependent dehydatase associated subunit
Family:Dehydratase-reactivating factor beta subunit
46c3rcqA_
not modelled 9.1 25 PDB header:oxidoreductase
Chain: A: PDB Molecule:aspartyl/asparaginyl beta-hydroxylase;
PDBTitle: crystal structure of human aspartate beta-hydroxylase isoform a
47c2qlwA_
not modelled 8.9 20 PDB header:isomerase
Chain: A: PDB Molecule:rhau;
PDBTitle: crystal structure of rhamnose mutarotase rhau of rhizobium2 leguminosarum
48c2qlxA_
not modelled 8.9 20 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
49d1vpha_
not modelled 8.7 14 Fold:YjbQ-like
Superfamily:YjbQ-like
Family:YjbQ-like
50c2p6cB_
not modelled 8.5 13 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.
51d1wiga2
not modelled 8.3 33 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:LIM domain
52d2g5ca2
not modelled 8.3 33 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
53c3dzbA_
not modelled 8.2 26 PDB header:biosynthetic protein
Chain: A: PDB Molecule:prephenate dehydrogenase;
PDBTitle: crystal structure of prephenate dehydrogenase from streptococcus2 thermophilus
54c2xr9A_
not modelled 7.8 11 PDB header:hydrolase
Chain: A: PDB Molecule:ectonucleotide pyrophosphatase/phosphodiesterase family
PDBTitle: crystal structure of autotaxin (enpp2)
55d1f6da_
not modelled 7.7 18 Fold:UDP-Glycosyltransferase/glycogen phosphorylase
Superfamily:UDP-Glycosyltransferase/glycogen phosphorylase
Family:UDP-N-acetylglucosamine 2-epimerase
56d1x8da1
not modelled 7.5 40 Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:YiiL-like
57c1vraA_
not modelled 7.4 10 PDB header:transferase
Chain: A: PDB Molecule:arginine biosynthesis bifunctional protein argj;
PDBTitle: crystal structure of arginine biosynthesis bifunctional protein argj2 (10175521) from bacillus halodurans at 2.00 a resolution
58c2g5cD_
not modelled 7.4 32 PDB header:oxidoreductase
Chain: D: PDB Molecule:prephenate dehydrogenase;
PDBTitle: crystal structure of prephenate dehydrogenase from aquifex aeolicus
59d1gv2a2
not modelled 7.4 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Myb/SANT domain
60d1f0ya2
not modelled 7.3 28 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
61c2pv7B_
not modelled 7.2 39 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
62c3sggA_
not modelled 7.1 7 PDB header:hydrolase
Chain: A: PDB Molecule:hypothetical hydrolase;
PDBTitle: crystal structure of a hypothetical hydrolase (bt_2193) from2 bacteroides thetaiotaomicron vpi-5482 at 1.25 a resolution
63c1idzA_
not modelled 7.0 24 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
64c3kowH_
not modelled 6.9 20 PDB header:metal binding protein
Chain: H: PDB Molecule:d-ornithine aminomutase s component;
PDBTitle: crystal structure of ornithine 4,5 aminomutase backsoaked complex
65c3ggpA_
not modelled 6.8 32 PDB header:oxidoreductase
Chain: A: PDB Molecule:prephenate dehydrogenase;
PDBTitle: crystal structure of prephenate dehydrogenase from a. aeolicus in2 complex with hydroxyphenyl propionate and nad+
66d1dm5a_
not modelled 6.8 19 Fold:Annexin
Superfamily:Annexin
Family:Annexin
67d1at3a_
not modelled 6.7 30 Fold:Herpes virus serine proteinase, assemblin
Superfamily:Herpes virus serine proteinase, assemblin
Family:Herpes virus serine proteinase, assemblin
68d2csba2
not modelled 6.7 21 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:Topoisomerase V repeat domain
69c2wasA_
not modelled 6.6 25 PDB header:transferase
Chain: A: PDB Molecule:3-oxoacyl-[acyl-carrier-protein] synthase;
PDBTitle: structure of the fungal type i fas ppt domain
70d1wdka3
not modelled 6.6 39 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
71d2pgda2
not modelled 6.6 28 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
72d1hm6a_
not modelled 6.5 18 Fold:Annexin
Superfamily:Annexin
Family:Annexin
73d1nbwb_
not modelled 6.4 25 Fold:Anticodon-binding domain-like
Superfamily:B12-dependent dehydatase associated subunit
Family:Dehydratase-reactivating factor beta subunit
74c2ep9A_
not modelled 6.3 33 PDB header:oxidoreductase
Chain: A: PDB Molecule:l-gulonate 3-dehydrogenase;
PDBTitle: crystal structure of the rabbit l-gulonate 3-dehydrogenase2 (nadh form)
75d1chua3
not modelled 6.2 15 Fold:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Superfamily:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Family:Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
76c3crw1_
not modelled 6.2 16 PDB header:hydrolase
Chain: 1: PDB Molecule:xpd/rad3 related dna helicase;
PDBTitle: "xpd_apo"
77d1eexb_
not modelled 6.1 22 Fold:Anticodon-binding domain-like
Superfamily:B12-dependent dehydatase associated subunit
Family:Diol dehydratase, beta subunit
78d1vzva_
not modelled 5.9 30 Fold:Herpes virus serine proteinase, assemblin
Superfamily:Herpes virus serine proteinase, assemblin
Family:Herpes virus serine proteinase, assemblin
79c2c1fA_
not modelled 5.9 22 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
80d1i36a2
not modelled 5.9 28 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
81c2h1zA_
not modelled 5.9 50 PDB header:toxin
Chain: A: PDB Molecule:hybrid atracotoxin;
PDBTitle: structure of a dual-target spider toxin
82d1wo8a1
not modelled 5.8 13 Fold:Methylglyoxal synthase-like
Superfamily:Methylglyoxal synthase-like
Family:Methylglyoxal synthase, MgsA
83d1hrti_
not modelled 5.8 40 Fold:Knottins (small inhibitors, toxins, lectins)
Superfamily:Leech antihemostatic proteins
Family:Hirudin-like
84c2v4iA_
not modelled 5.8 6 PDB header:transferase
Chain: A: PDB Molecule:glutamate n-acetyltransferase 2 alpha chain;
PDBTitle: structure of a novel n-acyl-enzyme intermediate of an n-2 terminal nucleophile (ntn) hydrolase, oat2
85d1zeta1
not modelled 5.8 20 Fold:Lesion bypass DNA polymerase (Y-family), little finger domain
Superfamily:Lesion bypass DNA polymerase (Y-family), little finger domain
Family:Lesion bypass DNA polymerase (Y-family), little finger domain
86d3cuma2
not modelled 5.8 35 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
87c2dwuA_
not modelled 5.8 15 PDB header:isomerase
Chain: A: PDB Molecule:glutamate racemase;
PDBTitle: crystal structure of glutamate racemase isoform race1 from bacillus2 anthracis
88d1mbja_
not modelled 5.8 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Myb/SANT domain
89c1mbjA_
not modelled 5.8 21 PDB header:dna binding protein
Chain: A: PDB Molecule:myb proto-oncogene protein;
PDBTitle: mouse c-myb dna-binding domain repeat 3
90c2rpaA_
not modelled 5.8 12 PDB header:hydrolase
Chain: A: PDB Molecule:katanin p60 atpase-containing subunit a1;
PDBTitle: the solution structure of n-terminal domain of microtubule severing2 enzyme
91d1sfkb_
not modelled 5.7 20 Fold:Flavivirus capsid protein C
Superfamily:Flavivirus capsid protein C
Family:Flavivirus capsid protein C
92d1uoua1
not modelled 5.7 18 Fold:Methionine synthase domain-like
Superfamily:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
Family:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
93c3njqB_
not modelled 5.7 30 PDB header:viral protein/inhibitor
Chain: B: PDB Molecule:orf 17;
PDBTitle: crystal structure of kaposi's sarcoma-associated herpesvirus protease2 in complex with dimer disruptor
94d1m9ia2
not modelled 5.7 22 Fold:Annexin
Superfamily:Annexin
Family:Annexin
95c2p6uA_
not modelled 5.7 36 PDB header:dna binding protein
Chain: A: PDB Molecule:afuhel308 helicase;
PDBTitle: apo structure of the hel308 superfamily 2 helicase
96c2rafC_
not modelled 5.7 17 PDB header:oxidoreductase
Chain: C: PDB Molecule:putative dinucleotide-binding oxidoreductase;
PDBTitle: crystal structure of putative dinucleotide-binding2 oxidoreductase (np_786167.1) from lactobacillus plantarum3 at 1.60 a resolution
97d1h4ga_
not modelled 5.6 17 Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Xylanase/endoglucanase 11/12
98d2pv7a2
not modelled 5.6 44 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:6-phosphogluconate dehydrogenase-like, N-terminal domain
99c2ysrA_
not modelled 5.6 17 PDB header:signaling protein
Chain: A: PDB Molecule:dep domain-containing protein 1;
PDBTitle: solution structure of the dep domain from human dep domain-2 containing protein 1

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