Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP10443
DateThu Jan 5 11:32:19 GMT 2012
Unique Job ID42bb57e9b22d4d14

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3e0dA_
Top template information
PDB header:transferase/dna
Chain: A: PDB Molecule:dna polymerase iii subunit alpha;
PDBTitle: insights into the replisome from the crystral structure of2 the ternary complex of the eubacterial dna polymerase iii3 alpha-subunit
Confidence and coverage
Confidence:100.0% Coverage: 93%
1084 residues ( 93% 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  MSEPRFVHLRVHSDYSMIDGLAKTAPLVKKAAALGMPALAITDFTNLCGLVKFYGAGHGA
Secondary structure 



















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Disorder  ????
?












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   .........70.........80.........90.........100.........110.........120
Sequence  GIKPIVGADFNVQCDLLGDELTHLTVLAANNTGYQNLTLLISKAYQRGYGAAGPIIDRDW
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?

??????







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   .........130.........140.........150.........160.........170.........180
Sequence  LIELNEGLILLSGGRMGDVGRSLLRGNSALVDECVAFYEEHFPDRYFLELIRTGRPDEES
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   .........190.........200.........210.........220.........230.........240
Sequence  YLHAAVELAEARGLPVVATNDVRFIDSSDFDAHEIRVAIHDGFTLDDPKRPRNYSPQQYM
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   .........250.........260.........270.........280.........290.........300
Sequence  RSEEEMCELFADIPEALANTVEIAKRCNVTVRLGEYFLPQFPTGDMSTEDYLVKRAKEGL
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   .........310.........320.........330.........340.........350.........360
Sequence  EERLAFLFPDEEERLKRRPEYDERLETELQVINQMGFPGYFLIVMEFIQWSKDNGVPVGP
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   .........370.........380.........390.........400.........410.........420
Sequence  GRGSGAGSLVAYALKITDLDPLEFDLLFERFLNPERVSMPDFDVDFCMEKRDQVIEHVAD
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   .........430.........440.........450.........460.........470.........480
Sequence  MYGRDAVSQIITFGTMAAKAVIRDVGRVLGHPYGFVDRISKLIPPDPGMTLAKAFEAEPQ
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   .........490.........500.........510.........520.........530.........540
Sequence  LPEIYEADEEVKALIDMARKLEGVTRNAGKHAGGVVIAPTKITDFAPLYCDEEGKHPVTQ
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Disorder  ?

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   .........550.........560.........570.........580.........590.........600
Sequence  FDKSDVEYAGLVKFDFLGLRTLTIINWALEMINKRRAKNGEPPLDIAAIPLDDKKSFDML
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   .........610.........620.........630.........640.........650.........660
Sequence  QRSETTAVFQLESRGMKDLIKRLQPDCFEDMIALVALFRPGPLQSGMVDNFIDRKHGREE
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   .........670.........680.........690.........700.........710.........720
Sequence  ISYPDVQWQHESLKPVLEPTYGIILYQEQVMQIAQVLSGYTLGGADMLRRAMGKKKPEEM
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   .........730.........740.........750.........760.........770.........780
Sequence  AKQRSVFAEGAEKNGINAELAMKIFDLVEKFAGYGFNKSHSAAYALVSYQTLWLKAHYPA
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   .........790.........800.........810.........820.........830.........840
Sequence  EFMAAVMTADMDNTEKVVGLVDECWRMGLKILPPDINSGLYHFHVNDDGEIVYGIGAIKG
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   .........850.........860.........870.........880.........890.........900
Sequence  VGEGPIEAIIEARNKGGYFRELFDLCARTDTKKLNRRVLEKLIMSGAFDRLGPHRAALMN
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   .........910.........920.........930.........940.........950.........960
Sequence  SLGDALKAADQHAKAEAIGQADMFGVLAEEPEQIEQSYASCQPWPEQVVLDGERETLGLY
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??????????????????????????






















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   .........970.........980.........990.........1000.........1010.........1020
Sequence  LTGHPINQYLKEIERYVGGVRLKDMHPTERGKVITAAGLVVAARVMVTKRGNRIGICTLD
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   .........1030.........1040.........1050.........1060.........1070.........1080
Sequence  DRSGRLEVMLFTDALDKYQQLLEKDRILIVSGQVSFDDFSGGLKMTAREVMDIDEAREKY
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   .........1090.........1100.........1110.........1120.........1130.........1140
Sequence  ARGLAISLTDRQIDDQLLNRLRQSLEPHRSGTIPVHLYYQRADARARLRFGATWRVSPSD
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   .........1150.........1160
Sequence  RLLNDLRGLIGSEQVELEFD
Secondary structure 





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??
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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 3e0d chain A

3D model

Region: 1 - 1140
Aligned: 1084
Modelled: 1084
Confidence: 100.0%
Identity: 42%
PDB header:transferase/dna
Chain: A: PDB Molecule:dna polymerase iii subunit alpha;
PDBTitle: insights into the replisome from the crystral structure of2 the ternary complex of the eubacterial dna polymerase iii3 alpha-subunit

Phyre2

PDB 2hnh chain A

3D model

Region: 1 - 910
Aligned: 910
Modelled: 910
Confidence: 100.0%
Identity: 100%
PDB header:transferase
Chain: A: PDB Molecule:dna polymerase iii alpha subunit;
PDBTitle: crystal structure of the catalytic alpha subunit of e. coli2 replicative dna polymerase iii

Phyre2

PDB 3f2c chain A

3D model

Region: 3 - 900
Aligned: 786
Modelled: 832
Confidence: 100.0%
Identity: 27%
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

Phyre2

PDB 3e0f chain A

3D model

Region: 9 - 299
Aligned: 250
Modelled: 252
Confidence: 99.8%
Identity: 18%
PDB header:hydrolase
Chain: A: PDB Molecule:putative metal-dependent phosphoesterase;
PDBTitle: crystal structure of a putative metal-dependent phosphoesterase2 (bad_1165) from bifidobacterium adolescentis atcc 15703 at 2.40 a3 resolution

Phyre2

PDB 2wje chain A

3D model

Region: 6 - 263
Aligned: 211
Modelled: 221
Confidence: 99.7%
Identity: 18%
PDB header:hydrolase
Chain: A: PDB Molecule:tyrosine-protein phosphatase cpsb;
PDBTitle: crystal structure of the tyrosine phosphatase cps4b from2 steptococcus pneumoniae tigr4.

Phyre2

PDB 2yb1 chain A

3D model

Region: 7 - 208
Aligned: 186
Modelled: 202
Confidence: 99.7%
Identity: 20%
PDB header:hydrolase
Chain: A: PDB Molecule:amidohydrolase;
PDBTitle: structure of an amidohydrolase from chromobacterium violaceum (efi2 target efi-500202) with bound mn, amp and phosphate.

Phyre2

PDB 3qy6 chain A

3D model

Region: 6 - 286
Aligned: 220
Modelled: 220
Confidence: 99.7%
Identity: 14%
PDB header:hydrolase
Chain: A: PDB Molecule:tyrosine-protein phosphatase ywqe;
PDBTitle: crystal structures of ywqe from bacillus subtilis and cpsb from2 streptococcus pneumoniae, unique metal-dependent tyrosine3 phosphatases

Phyre2

PDB 3dcp chain B

3D model

Region: 9 - 206
Aligned: 197
Modelled: 195
Confidence: 99.7%
Identity: 18%
PDB header:hydrolase
Chain: B: PDB Molecule:histidinol-phosphatase;
PDBTitle: crystal structure of the putative histidinol phosphatase2 hisk from listeria monocytogenes. northeast structural3 genomics consortium target lmr141.

Phyre2

PDB 2yz5 chain B

3D model

Region: 7 - 220
Aligned: 207
Modelled: 214
Confidence: 99.6%
Identity: 16%
PDB header:hydrolase
Chain: B: PDB Molecule:histidinol phosphatase;
PDBTitle: histidinol phosphate phosphatase complexed with phosphate

Phyre2

PDB 1m65 chain A

3D model

Region: 7 - 249
Aligned: 219
Modelled: 243
Confidence: 99.4%
Identity: 16%
Fold: 7-stranded beta/alpha barrel
Superfamily: PHP domain-like
Family: PHP domain

Phyre2

PDB 2anu chain A domain 1

3D model

Region: 6 - 225
Aligned: 174
Modelled: 181
Confidence: 99.2%
Identity: 18%
Fold: 7-stranded beta/alpha barrel
Superfamily: PHP domain-like
Family: PHP domain

Phyre2

PDB 2anu chain A

3D model

Region: 6 - 225
Aligned: 174
Modelled: 176
Confidence: 99.2%
Identity: 18%
PDB header:metal binding protein
Chain: A: PDB Molecule:hypothetical protein tm0559;
PDBTitle: crystal structure of predicted metal-dependent phosphoesterase (php2 family) (tm0559) from thermotoga maritima at 2.40 a resolution

Phyre2

PDB 2w9m chain B

3D model

Region: 9 - 227
Aligned: 194
Modelled: 203
Confidence: 99.0%
Identity: 16%
PDB header:dna replication
Chain: B: PDB Molecule:polymerase x;
PDBTitle: structure of family x dna polymerase from deinococcus2 radiodurans

Phyre2

PDB 3e38 chain A

3D model

Region: 6 - 87
Aligned: 75
Modelled: 82
Confidence: 98.9%
Identity: 21%
PDB header:hydrolase
Chain: A: PDB Molecule:two-domain protein containing predicted php-like metal-
PDBTitle: crystal structure of a two-domain protein containing predicted php-2 like metal-dependent phosphoesterase (bvu_3505) from bacteroides3 vulgatus atcc 8482 at 2.20 a resolution

Phyre2

PDB 1c0a chain A domain 1

3D model

Region: 978 - 1073
Aligned: 91
Modelled: 96
Confidence: 97.9%
Identity: 24%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Anticodon-binding domain

Phyre2

PDB 3i7f chain A

3D model

Region: 980 - 1081
Aligned: 97
Modelled: 102
Confidence: 97.8%
Identity: 14%
PDB header:ligase
Chain: A: PDB Molecule:aspartyl-trna synthetase;
PDBTitle: aspartyl trna synthetase from entamoeba histolytica

Phyre2

PDB 1b8a chain B

3D model

Region: 978 - 1081
Aligned: 98
Modelled: 104
Confidence: 97.8%
Identity: 16%
PDB header:ligase
Chain: B: PDB Molecule:protein (aspartyl-trna synthetase);
PDBTitle: aspartyl-trna synthetase

Phyre2

PDB 1b8a chain A domain 1

3D model

Region: 977 - 1076
Aligned: 95
Modelled: 100
Confidence: 97.8%
Identity: 19%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Anticodon-binding domain

Phyre2

PDB 1x55 chain A

3D model

Region: 978 - 1071
Aligned: 89
Modelled: 94
Confidence: 97.7%
Identity: 20%
PDB header:ligase
Chain: A: PDB Molecule:asparaginyl-trna synthetase;
PDBTitle: crystal structure of asparaginyl-trna synthetase from pyrococcus2 horikoshii complexed with asparaginyl-adenylate analogue

Phyre2

PDB 1e1o chain A domain 1

3D model

Region: 991 - 1081
Aligned: 85
Modelled: 91
Confidence: 97.7%
Identity: 19%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Anticodon-binding domain

Phyre2
1

c3e0dA_
2

c2hnhA_
3

c3f2cA_
4

c3e0fA_
5

c2wjeA_
6

c2yb1A_
7

c3qy6A_
8

c3dcpB_
9

c2yz5B_
10

d1m65a_
11

d2anua1
12

c2anuA_
13

c2w9mB_
14

c3e38A_
15

d1c0aa1
16

c3i7fA_
17

c1b8aB_
18

d1b8aa1
19

c1x55A_
20

d1e1oa1
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3e0dA_



100.0 42 PDB header:transferase/dna
Chain: A: PDB Molecule:dna polymerase iii subunit alpha;
PDBTitle: insights into the replisome from the crystral structure of2 the ternary complex of the eubacterial dna polymerase iii3 alpha-subunit
2c2hnhA_



100.0 100 PDB header:transferase
Chain: A: PDB Molecule:dna polymerase iii alpha subunit;
PDBTitle: crystal structure of the catalytic alpha subunit of e. coli2 replicative dna polymerase iii
3c3f2cA_



100.0 27 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
4c3e0fA_



99.8 18 PDB header:hydrolase
Chain: A: PDB Molecule:putative metal-dependent phosphoesterase;
PDBTitle: crystal structure of a putative metal-dependent phosphoesterase2 (bad_1165) from bifidobacterium adolescentis atcc 15703 at 2.40 a3 resolution
5c2wjeA_



99.7 18 PDB header:hydrolase
Chain: A: PDB Molecule:tyrosine-protein phosphatase cpsb;
PDBTitle: crystal structure of the tyrosine phosphatase cps4b from2 steptococcus pneumoniae tigr4.
6c2yb1A_



99.7 20 PDB header:hydrolase
Chain: A: PDB Molecule:amidohydrolase;
PDBTitle: structure of an amidohydrolase from chromobacterium violaceum (efi2 target efi-500202) with bound mn, amp and phosphate.
7c3qy6A_



99.7 14 PDB header:hydrolase
Chain: A: PDB Molecule:tyrosine-protein phosphatase ywqe;
PDBTitle: crystal structures of ywqe from bacillus subtilis and cpsb from2 streptococcus pneumoniae, unique metal-dependent tyrosine3 phosphatases
8c3dcpB_



99.7 18 PDB header:hydrolase
Chain: B: PDB Molecule:histidinol-phosphatase;
PDBTitle: crystal structure of the putative histidinol phosphatase2 hisk from listeria monocytogenes. northeast structural3 genomics consortium target lmr141.
9c2yz5B_



99.6 16 PDB header:hydrolase
Chain: B: PDB Molecule:histidinol phosphatase;
PDBTitle: histidinol phosphate phosphatase complexed with phosphate
10d1m65a_



99.4 16 Fold:7-stranded beta/alpha barrel
Superfamily:PHP domain-like
Family:PHP domain
11d2anua1



99.2 18 Fold:7-stranded beta/alpha barrel
Superfamily:PHP domain-like
Family:PHP domain
12c2anuA_



99.2 18 PDB header:metal binding protein
Chain: A: PDB Molecule:hypothetical protein tm0559;
PDBTitle: crystal structure of predicted metal-dependent phosphoesterase (php2 family) (tm0559) from thermotoga maritima at 2.40 a resolution
13c2w9mB_



99.0 16 PDB header:dna replication
Chain: B: PDB Molecule:polymerase x;
PDBTitle: structure of family x dna polymerase from deinococcus2 radiodurans
14c3e38A_



98.9 21 PDB header:hydrolase
Chain: A: PDB Molecule:two-domain protein containing predicted php-like metal-
PDBTitle: crystal structure of a two-domain protein containing predicted php-2 like metal-dependent phosphoesterase (bvu_3505) from bacteroides3 vulgatus atcc 8482 at 2.20 a resolution
15d1c0aa1



97.9 24 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Anticodon-binding domain
16c3i7fA_



97.8 14 PDB header:ligase
Chain: A: PDB Molecule:aspartyl-trna synthetase;
PDBTitle: aspartyl trna synthetase from entamoeba histolytica
17c1b8aB_



97.8 16 PDB header:ligase
Chain: B: PDB Molecule:protein (aspartyl-trna synthetase);
PDBTitle: aspartyl-trna synthetase
18d1b8aa1



97.8 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Anticodon-binding domain
19c1x55A_



97.7 20 PDB header:ligase
Chain: A: PDB Molecule:asparaginyl-trna synthetase;
PDBTitle: crystal structure of asparaginyl-trna synthetase from pyrococcus2 horikoshii complexed with asparaginyl-adenylate analogue
20d1e1oa1



97.7 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Anticodon-binding domain
21d1gm5a2



not modelled 97.7 14 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:RecG "wedge" domain
22c1eqrC_



not modelled 97.6 22 PDB header:ligase
Chain: C: PDB Molecule:aspartyl-trna synthetase;
PDBTitle: crystal structure of free aspartyl-trna synthetase from2 escherichia coli
23c3e9hB_



not modelled 97.6 15 PDB header:ligase
Chain: B: PDB Molecule:lysyl-trna synthetase;
PDBTitle: lysyl-trna synthetase from bacillus stearothermophilus2 complexed with l-lysylsulfamoyl adenosine
24d1bbua1



not modelled 97.6 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Anticodon-binding domain
25c1wydB_



not modelled 97.6 23 PDB header:ligase
Chain: B: PDB Molecule:hypothetical aspartyl-trna synthetase;
PDBTitle: crystal structure of aspartyl-trna synthetase from sulfolobus tokodaii
26c3bjuB_



not modelled 97.5 19 PDB header:ligase
Chain: B: PDB Molecule:lysyl-trna synthetase;
PDBTitle: crystal structure of tetrameric form of human lysyl-trna2 synthetase
27d1n9wa1



not modelled 97.5 31 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Anticodon-binding domain
28d1l0wa1



not modelled 97.5 14 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Anticodon-binding domain
29c2xgtB_



not modelled 97.5 18 PDB header:ligase
Chain: B: PDB Molecule:asparaginyl-trna synthetase, cytoplasmic;
PDBTitle: asparaginyl-trna synthetase from brugia malayi complexed2 with the sulphamoyl analogue of asparaginyl-adenylate
30c3kf6A_



not modelled 97.5 19 PDB header:structural protein
Chain: A: PDB Molecule:protein stn1;
PDBTitle: crystal structure of s. pombe stn1-ten1 complex
31c3dm3A_



not modelled 97.5 22 PDB header:replication
Chain: A: PDB Molecule:replication factor a;
PDBTitle: crystal structure of a domain of a replication factor a2 protein, from methanocaldococcus jannaschii. northeast3 structural genomics target mjr118e
32c2k50A_



not modelled 97.4 16 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:replication factor a related protein;
PDBTitle: solution nmr structure of the replication factor a related2 protein from methanobacterium thermoautotrophicum.3 northeast structural genomics target tr91a.
33c1efwA_



not modelled 97.4 14 PDB header:ligase/rna
Chain: A: PDB Molecule:aspartyl-trna synthetase;
PDBTitle: crystal structure of aspartyl-trna synthetase from thermus2 thermophilus complexed to trnaasp from escherichia coli
34d1eova1



not modelled 97.4 20 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Anticodon-binding domain
35c3m4qA_



not modelled 97.3 22 PDB header:ligase
Chain: A: PDB Molecule:asparaginyl-trna synthetase, putative;
PDBTitle: entamoeba histolytica asparaginyl-trna synthetase (asnrs)
36c1e22A_



not modelled 97.3 17 PDB header:ligase
Chain: A: PDB Molecule:lysyl-trna synthetase;
PDBTitle: lysyl-trna synthetase (lysu) hexagonal form complexed with2 lysine and the non-hydrolysable atp analogue amp-pcp
37d2edua1



not modelled 97.2 16 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:ComEA-like
38c3e0eA_



not modelled 97.2 23 PDB header:replication
Chain: A: PDB Molecule:replication protein a;
PDBTitle: crystal structure of a domain of replication protein a from2 methanococcus maripaludis. northeast structural genomics3 targe mrr110b
39c1asyA_



not modelled 97.1 20 PDB header:complex (aminoacyl-trna synthase/trna)
Chain: A: PDB Molecule:aspartyl-trna synthetase;
PDBTitle: class ii aminoacyl transfer rna synthetases: crystal2 structure of yeast aspartyl-trna synthetase complexed with3 trna asp
40c1n9wA_



not modelled 97.1 33 PDB header:biosynthetic protein
Chain: A: PDB Molecule:aspartyl-trna synthetase 2;
PDBTitle: crystal structure of the non-discriminating and archaeal-2 type aspartyl-trna synthetase from thermus thermophilus
41d2pi2a1



not modelled 96.8 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
42d1o7ia_



not modelled 96.8 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
43c1z9fA_



not modelled 96.8 18 PDB header:dna binding protein
Chain: A: PDB Molecule:single-strand binding protein;
PDBTitle: crystal structure of single stranded dna-binding protein (tm0604) from2 thermotoga maritima at 2.60 a resolution
44c1gm5A_



not modelled 96.8 14 PDB header:helicase
Chain: A: PDB Molecule:recg;
PDBTitle: structure of recg bound to three-way dna junction
45c2pi2A_



not modelled 96.7 21 PDB header:replication, dna binding protein
Chain: A: PDB Molecule:replication protein a 32 kda subunit;
PDBTitle: full-length replication protein a subunits rpa14 and rpa32
46d2i5ha1



not modelled 96.7 27 Fold:AF1531-like
Superfamily:AF1531-like
Family:AF1531-like
47c2i5hA_



not modelled 96.7 27 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein af1531;
PDBTitle: crystal structure of af1531 from archaeoglobus fulgidus,2 pfam duf655
48c3eivB_



not modelled 96.4 22 PDB header:dna binding protein
Chain: B: PDB Molecule:single-stranded dna-binding protein 2;
PDBTitle: crystal structure of single-stranded dna-binding protein2 from streptomyces coelicolor
49d1xjva1



not modelled 96.4 12 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
50d1krta_



not modelled 96.2 23 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Anticodon-binding domain
51d1qvca_



not modelled 96.2 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
52c2kenA_



not modelled 96.1 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:conserved protein;
PDBTitle: solution nmr structure of the ob domain (residues 67-166)2 of mm0293 from methanosarcina mazei. northeast structural3 genomics consortium target mar214a.
53c3tqyA_



not modelled 96.1 24 PDB header:transferase
Chain: A: PDB Molecule:single-stranded dna-binding protein;
PDBTitle: structure of a single-stranded dna-binding protein (ssb), from2 coxiella burnetii
54c1ynxA_



not modelled 96.1 18 PDB header:dna binding protein
Chain: A: PDB Molecule:replication factor-a protein 1;
PDBTitle: solution structure of dna binding domain a (dbd-a) of2 s.cerevisiae replication protein a (rpa)
55d1v1qa_



not modelled 96.0 12 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
56c3kf8C_



not modelled 95.9 13 PDB header:structural protein
Chain: C: PDB Molecule:protein stn1;
PDBTitle: crystal structure of c. tropicalis stn1-ten1 complex
57d1eyga_



not modelled 95.9 17 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
58c2ihfA_



not modelled 95.9 21 PDB header:dna binding protein
Chain: A: PDB Molecule:single-stranded dna-binding protein;
PDBTitle: crystal structure of deletion mutant delta 228-252 r190a of the2 single-stranded dna binding protein from thermus aquaticus
59d1jmca1



not modelled 95.7 23 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
60d1jmca2



not modelled 95.7 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
61c3pgzB_



not modelled 95.6 14 PDB header:dna binding protein
Chain: B: PDB Molecule:single-stranded dna-binding protein;
PDBTitle: crystal structure of a single strand binding protein (ssb) from2 bartonella henselae
62c1fguA_



not modelled 95.6 24 PDB header:replication
Chain: A: PDB Molecule:replication protein a 70 kda dna-binding subunit;
PDBTitle: ssdna-binding domain of the large subunit of replication2 protein a
63c2k75A_



not modelled 95.5 13 PDB header:dna binding protein
Chain: A: PDB Molecule:uncharacterized protein ta0387;
PDBTitle: solution nmr structure of the ob domain of ta0387 from2 thermoplasma acidophilum. northeast structural genomics3 consortium target tar80b.
64c1se8A_



not modelled 95.5 12 PDB header:dna binding protein
Chain: A: PDB Molecule:single-strand binding protein;
PDBTitle: structure of single-stranded dna-binding protein (ssb) from d.2 radiodurans
65d1se8a_



not modelled 95.5 12 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
66c1xjvA_



not modelled 95.4 12 PDB header:transcription/dna
Chain: A: PDB Molecule:protection of telomeres 1;
PDBTitle: crystal structure of human pot1 bound to telomeric single-2 stranded dna (ttagggttag)
67d1ue1a_



not modelled 95.4 23 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
68c2iheA_



not modelled 95.0 23 PDB header:dna binding protein
Chain: A: PDB Molecule:single-stranded dna-binding protein;
PDBTitle: crystal structure of wild-type single-stranded dna binding protein2 from thermus aquaticus
69c3kojA_



not modelled 95.0 14 PDB header:dna binding protein
Chain: A: PDB Molecule:uncharacterized protein ycf41;
PDBTitle: crystal structure of the ssb domain of q5n255_synp6 protein2 from synechococcus sp. northeast structural genomics3 consortium target snr59a.
70c3e0jG_



not modelled 94.9 19 PDB header:transferase
Chain: G: PDB Molecule:dna polymerase subunit delta-2;
PDBTitle: x-ray structure of the complex of regulatory subunits of2 human dna polymerase delta
71d3bzka1



not modelled 94.9 22 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:Tex HhH-containing domain-like
72d3ulla_



not modelled 94.9 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
73c1k8gC_



not modelled 94.7 14 PDB header:dna binding protein/dna
Chain: C: PDB Molecule:telomere-binding protein alpha subunit;
PDBTitle: crystal structure of the n-terminal domain of oxytricha2 nova telomere end binding protein alpha subunit both3 uncomplexed and complexed with telomeric ssdna
74c2vw9B_



not modelled 94.7 15 PDB header:dna-binding protein
Chain: B: PDB Molecule:single-stranded dna binding protein;
PDBTitle: single stranded dna binding protein complex from2 helicobacter pylori
75d1wjja_



not modelled 94.6 22 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
76c3lgjA_



not modelled 94.4 10 PDB header:dna binding protein
Chain: A: PDB Molecule:single-stranded dna-binding protein;
PDBTitle: crystal structure of single-stranded binding protein (ssb) from2 bartonella henselae
77c1s5lu_



not modelled 94.2 17 PDB header:photosynthesis
Chain: U: PDB Molecule:photosystem ii 12 kda extrinsic protein;
PDBTitle: architecture of the photosynthetic oxygen evolving center
78d1qzga_



not modelled 94.2 15 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
79d1jb7a1



not modelled 93.8 15 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
80c1ue7A_



not modelled 93.6 21 PDB header:dna binding protein
Chain: A: PDB Molecule:single-strand binding protein;
PDBTitle: crystal structure of the single-stranded dna-binding2 protein from mycobacterium tuberculosis
81c3fhwB_



not modelled 92.5 14 PDB header:dna binding protein
Chain: B: PDB Molecule:primosomal replication protein n;
PDBTitle: crystal structure of the protein prib from bordetella parapertussis.2 northeast structural genomics consortium target bpr162.
82c3k8aA_



not modelled 92.4 15 PDB header:dna binding protein
Chain: A: PDB Molecule:putative primosomal replication protein;
PDBTitle: neisseria gonorrhoeae prib
83d2axtu1



not modelled 92.2 17 Fold:SAM domain-like
Superfamily:PsbU/PolX domain-like
Family:PsbU-like
84d2duya1



not modelled 91.9 29 Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:ComEA-like
85c1eqqD_



not modelled 91.2 20 PDB header:replication/rna
Chain: D: PDB Molecule:single stranded dna binding protein;
PDBTitle: single stranded dna binding protein and ssdna complex
86c2ekcA_



not modelled 89.3 8 PDB header:lyase
Chain: A: PDB Molecule:tryptophan synthase alpha chain;
PDBTitle: structural study of project id aq_1548 from aquifex aeolicus vf5
87c2oceA_



not modelled 89.3 18 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein pa5201;
PDBTitle: crystal structure of tex family protein pa5201 from2 pseudomonas aeruginosa
88d1txya_



not modelled 88.7 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
89c1ph4A_



not modelled 87.4 14 PDB header:dna binding protein/dna
Chain: A: PDB Molecule:telomere-binding protein alpha subunit;
PDBTitle: crystal structure of the oxytricha nova telomere end-binding protein2 complexed with noncognate ssdna ggggttttggcg
90c1jb7A_



not modelled 87.4 14 PDB header:dna-binding protein/dna
Chain: A: PDB Molecule:telomere-binding protein alpha subunit;
PDBTitle: dna g-quartets in a 1.86 a resolution structure of an oxytricha nova2 telomeric protein-dna complex
91d1sr3a_



not modelled 86.7 21 Fold:OB-fold
Superfamily:Heme chaperone CcmE
Family:Heme chaperone CcmE
92c3en2A_



not modelled 81.8 16 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:probable primosomal replication protein n;
PDBTitle: three-dimensional structure of the protein prib from2 ralstonia solanacearum at the resolution 2.3a. northeast3 structural genomics consortium target rsr213c.
93d1hl9a2



not modelled 79.4 27 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Putative alpha-L-fucosidase, catalytic domain
94c1wxpA_



not modelled 79.0 19 PDB header:transport protein
Chain: A: PDB Molecule:tho complex subunit 1;
PDBTitle: solution structure of the death domain of nuclear matrix2 protein p84
95d1j6qa_



not modelled 75.7 24 Fold:OB-fold
Superfamily:Heme chaperone CcmE
Family:Heme chaperone CcmE
96c1j6qA_



not modelled 75.7 24 PDB header:chaperone
Chain: A: PDB Molecule:cytochrome c maturation protein e;
PDBTitle: solution structure and characterization of the heme2 chaperone ccme
97d2amxa1



not modelled 74.6 25 Fold:TIM beta/alpha-barrel
Superfamily:Metallo-dependent hydrolases
Family:Adenosine/AMP deaminase
98d1nnxa_



not modelled 74.1 12 Fold:OB-fold
Superfamily:Hypothetical protein YgiW
Family:Hypothetical protein YgiW
99d1vfla1



not modelled 72.3 33 Fold:TIM beta/alpha-barrel
Superfamily:Metallo-dependent hydrolases
Family:Adenosine/AMP deaminase
100c3rysA_



not modelled 70.9 23 PDB header:hydrolase
Chain: A: PDB Molecule:adenosine deaminase 1;
PDBTitle: the crystal structure of adenine deaminase (aaur1117) from2 arthrobacter aurescens
101d2qalk1



not modelled 70.6 28 Fold:Ribonuclease H-like motif
Superfamily:Translational machinery components
Family:Ribosomal protein L18 and S11
102c3jyvK_



not modelled 67.6 28 PDB header:ribosome
Chain: K: PDB Molecule:40s ribosomal protein s14(a);
PDBTitle: structure of the 40s rrna and proteins and p/e trna for eukaryotic2 ribosome based on cryo-em map of thermomyces lanuginosus ribosome at3 8.9a resolution
103c3mo4B_



not modelled 67.5 20 PDB header:hydrolase
Chain: B: PDB Molecule:alpha-1,3/4-fucosidase;
PDBTitle: the crystal structure of an alpha-(1-3,4)-fucosidase from2 bifidobacterium longum subsp. infantis atcc 15697
104c1hl8B_



not modelled 65.7 18 PDB header:hydrolase
Chain: B: PDB Molecule:putative alpha-l-fucosidase;
PDBTitle: crystal structure of thermotoga maritima alpha-fucosidase
105d1rh9a1



not modelled 64.3 16 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:beta-glycanases
106d1ug3a1



not modelled 64.2 17 Fold:alpha-alpha superhelix
Superfamily:ARM repeat
Family:MIF4G domain-like
107d1tg7a5



not modelled 62.7 19 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Glycosyl hydrolases family 35 catalytic domain
108d1ujpa_



not modelled 60.7 7 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
109d1a4ma_



not modelled 60.1 29 Fold:TIM beta/alpha-barrel
Superfamily:Metallo-dependent hydrolases
Family:Adenosine/AMP deaminase
110c2x6kB_



not modelled 60.1 18 PDB header:transferase
Chain: B: PDB Molecule:phosphotidylinositol 3 kinase 59f;
PDBTitle: the crystal structure of the drosophila class iii pi3-kinase2 vps34 in complex with pi-103
111d1geqa_



not modelled 59.3 20 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
112c3psiA_



not modelled 58.1 11 PDB header:transcription
Chain: A: PDB Molecule:transcription elongation factor spt6;
PDBTitle: crystal structure of the spt6 core domain from saccharomyces2 cerevisiae, form spt6(239-1451)
113d1wcga1



not modelled 58.1 15 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Family 1 of glycosyl hydrolase
114d1rpxa_



not modelled 57.3 13 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:D-ribulose-5-phosphate 3-epimerase
115c2dplA_



not modelled 56.4 19 PDB header:ligase
Chain: A: PDB Molecule:gmp synthase [glutamine-hydrolyzing] subunit b;
PDBTitle: crystal structure of the gmp synthase from pyrococcus horikoshii ot3
116d1i94m_



not modelled 55.1 15 Fold:S13-like H2TH domain
Superfamily:S13-like H2TH domain
Family:Ribosomal protein S13
117c3navB_



not modelled 54.7 16 PDB header:lyase
Chain: B: PDB Molecule:tryptophan synthase alpha chain;
PDBTitle: crystal structure of an alpha subunit of tryptophan synthase from2 vibrio cholerae o1 biovar el tor str. n16961
118d1hjqa_



not modelled 54.5 16 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:beta-glycanases
119c3pzqA_



not modelled 54.1 23 PDB header:hydrolase
Chain: A: PDB Molecule:mannan endo-1,4-beta-mannosidase. glycosyl hydrolase family
PDBTitle: structure of the hyperthermostable endo-1,4-beta-d-mannanase from2 thermotoga petrophila rku-1 with maltose and glycerol
120d2v4jc1



not modelled 53.9 21 Fold:DsrC, the gamma subunit of dissimilatory sulfite reductase
Superfamily:DsrC, the gamma subunit of dissimilatory sulfite reductase
Family:DsrC, the gamma subunit of dissimilatory sulfite reductase

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