Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP21513
DateThu Jan 5 11:38:24 GMT 2012
Unique Job ID45260adf866effd8

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2c4rL_
Top template information
PDB header:hydrolase
Chain: L: PDB Molecule:ribonuclease e;
PDBTitle: catalytic domain of e. coli rnase e
Confidence and coverage
Confidence:100.0% Coverage: 46%
484 residues ( 46% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
Warning: 60% of your sequence is predicted disordered. Disordered regions cannot be meaningfully predicted.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MKRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDY
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Disorder  ???



























???

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

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?
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   .........130.........140.........150.........160.........170.........180
Sequence  SLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEAL
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????

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   .........190.........200.........210.........220.........230.........240
Sequence  QWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELA
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   .........250.........260.........270.........280.........290.........300
Sequence  RQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALT
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   .........310.........320.........330.........340.........350.........360
Sequence  AIDINSARATRGGDIEETAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVE
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   .........370.........380.........390.........400.........410.........420
Sequence  NRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLS
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   .........430.........440.........450.........460.........470.........480
Sequence  LSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQME
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Disorder 









?????





























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?????
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   .........490.........500.........510.........520.........530.........540
Sequence  TPHYHVLRVRKGEETPTLSYMLPKLHEEAMALPSEEEFAERKRPEQPALATFAMPDVPPA
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Disorder 
????

?????????????????????????????????????????????????????
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   .........550.........560.........570.........580.........590.........600
Sequence  PTPAEPAAPVVAPAPKAAPATPAAPAQPGLLSRFFGALKALFSGGEETKPTEQPAPKAEA
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   .........610.........620.........630.........640.........650.........660
Sequence  KPERQQDRRKPRQNNRRDRNERRDTRSERTEGSDNREENRRNRRQAQQQTAETRESRQQA
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Disorder  ????????????????????????????????????????????????????????????
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   .........670.........680.........690.........700.........710.........720
Sequence  EVTEKARTADEQQAPRRERSRRRNDDKRQAQQEAKALNVEEQSVQETEQEERVRPVQPRR
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   .........730.........740.........750.........760.........770.........780
Sequence  KQRQLNQKVRYEQSVAEEAVVAPVVEETVAAEPIVQEAPAPRTELVKVPLPVVAQTAPEQ
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   .........790.........800.........810.........820.........830.........840
Sequence  QEENNADNRDNGGMPRRSRRSPRHLRVSGQRRRRYRDERYPTQSPMPLTVACASPELASG
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   .........850.........860.........870.........880.........890.........900
Sequence  KVWIRYPIVRPQDVQVEEQREQEEVHVQPMVTEVPVAAAIEPVVSAPVVEEVAGVVEAPV
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   .........910.........920.........930.........940.........950.........960
Sequence  QVAEPQPEVVETTHPEVIAAAVTEQPQVITESDVAVAQEVAEQAEPVVEPQEETADIEEV
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   .........970.........980.........990.........1000.........1010.........1020
Sequence  VETAEVVVAEPEVVAQPAAPVVAEVAAEVETVAAVEPEVTVEHNHATAPMTRAPAPEYVP
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   .........1030.........1040.........1050.........1060.
Sequence  EAPRHSDWQRPTFAFEGKGAAGGHTATHHASAAPARPQPVE
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Disorder  ?????????????????????????????????????????
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Confidence Key
High(9)                    Low (0)
?Disordered
Alpha helix
Beta strand

Domain analysis 

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

RankAligned region

PDB 2c4r chain L

3D model

Region: 1 - 503
Aligned: 484
Modelled: 503
Confidence: 100.0%
Identity: 100%
PDB header:hydrolase
Chain: L: PDB Molecule:ribonuclease e;
PDBTitle: catalytic domain of e. coli rnase e

Phyre2

PDB 1smx chain A

3D model

Region: 39 - 124
Aligned: 86
Modelled: 86
Confidence: 99.9%
Identity: 100%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2z0s chain A domain 1

3D model

Region: 36 - 125
Aligned: 82
Modelled: 90
Confidence: 98.3%
Identity: 15%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2cqo chain A

3D model

Region: 30 - 117
Aligned: 77
Modelled: 88
Confidence: 98.2%
Identity: 16%
PDB header:ribosome
Chain: A: PDB Molecule:nucleolar protein of 40 kda;
PDBTitle: solution structure of the s1 rna binding domain of human2 hypothetical protein flj11067

Phyre2

PDB 2ba0 chain A domain 1

3D model

Region: 36 - 119
Aligned: 73
Modelled: 84
Confidence: 98.2%
Identity: 21%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 1yz6 chain A

3D model

Region: 36 - 117
Aligned: 71
Modelled: 82
Confidence: 98.1%
Identity: 24%
PDB header:translation
Chain: A: PDB Molecule:probable translation initiation factor 2 alpha
PDBTitle: crystal structure of intact alpha subunit of aif2 from2 pyrococcus abyssi

Phyre2

PDB 1q46 chain A domain 2

3D model

Region: 37 - 119
Aligned: 72
Modelled: 83
Confidence: 98.1%
Identity: 18%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2z0s chain A

3D model

Region: 36 - 131
Aligned: 88
Modelled: 94
Confidence: 98.1%
Identity: 14%
PDB header:rna binding protein
Chain: A: PDB Molecule:probable exosome complex rna-binding protein 1;
PDBTitle: crystal structure of putative exosome complex rna-binding2 protein

Phyre2

PDB 2k4k chain A

3D model

Region: 33 - 118
Aligned: 75
Modelled: 86
Confidence: 98.1%
Identity: 23%
PDB header:rna binding protein
Chain: A: PDB Molecule:general stress protein 13;
PDBTitle: solution structure of gsp13 from bacillus subtilis

Phyre2

PDB 3bzk chain A domain 4

3D model

Region: 34 - 121
Aligned: 77
Modelled: 88
Confidence: 98.1%
Identity: 19%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2je6 chain I

3D model

Region: 16 - 119
Aligned: 95
Modelled: 104
Confidence: 98.0%
Identity: 19%
PDB header:hydrolase
Chain: I: PDB Molecule:exosome complex rna-binding protein 1;
PDBTitle: structure of a 9-subunit archaeal exosome

Phyre2

PDB 2khj chain A

3D model

Region: 28 - 119
Aligned: 81
Modelled: 92
Confidence: 98.0%
Identity: 25%
PDB header:ribosomal protein
Chain: A: PDB Molecule:30s ribosomal protein s1;
PDBTitle: nmr structure of the domain 6 of the e. coli ribosomal2 protein s1

Phyre2

PDB 2je6 chain I domain 1

3D model

Region: 36 - 125
Aligned: 81
Modelled: 90
Confidence: 98.0%
Identity: 21%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2khi chain A

3D model

Region: 29 - 119
Aligned: 81
Modelled: 81
Confidence: 98.0%
Identity: 14%
PDB header:ribosomal protein
Chain: A: PDB Molecule:30s ribosomal protein s1;
PDBTitle: nmr structure of the domain 4 of the e. coli ribosomal2 protein s1

Phyre2

PDB 2ba0 chain A

3D model

Region: 18 - 119
Aligned: 91
Modelled: 102
Confidence: 97.9%
Identity: 16%
PDB header:rna binding protein
Chain: A: PDB Molecule:archeal exosome rna binding protein rrp4;
PDBTitle: archaeal exosome core

Phyre2

PDB 2nn6 chain H domain 1

3D model

Region: 36 - 125
Aligned: 75
Modelled: 89
Confidence: 97.9%
Identity: 17%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 1q8k chain A

3D model

Region: 38 - 117
Aligned: 69
Modelled: 71
Confidence: 97.9%
Identity: 19%
PDB header:translation
Chain: A: PDB Molecule:eukaryotic translation initiation factor 2
PDBTitle: solution structure of alpha subunit of human eif2

Phyre2

PDB 2eqs chain A

3D model

Region: 31 - 106
Aligned: 66
Modelled: 68
Confidence: 97.9%
Identity: 38%
PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase dhx8;
PDBTitle: solution structure of the s1 rna binding domain of human2 atp-dependent rna helicase dhx8

Phyre2

PDB 1wi5 chain A

3D model

Region: 37 - 125
Aligned: 79
Modelled: 89
Confidence: 97.9%
Identity: 22%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 1sro chain A

3D model

Region: 35 - 119
Aligned: 73
Modelled: 85
Confidence: 97.9%
Identity: 32%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2
1

c2c4rL_
2

d1smxa_
3

d2z0sa1
4

c2cqoA_
5

d2ba0a1
6

c1yz6A_
7

d1q46a2
8

c2z0sA_
9

c2k4kA_
10

d3bzka4
11

c2je6I_
12

c2khjA_
13

d2je6i1
14

c2khiA_
15

c2ba0A_
16

d2nn6h1
17

c1q8kA_
18

c2eqsA_
19

d1wi5a_
20

d1sroa_
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2c4rL_



100.0 100 PDB header:hydrolase
Chain: L: PDB Molecule:ribonuclease e;
PDBTitle: catalytic domain of e. coli rnase e
2d1smxa_



99.9 100 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
3d2z0sa1



98.3 15 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
4c2cqoA_



98.2 16 PDB header:ribosome
Chain: A: PDB Molecule:nucleolar protein of 40 kda;
PDBTitle: solution structure of the s1 rna binding domain of human2 hypothetical protein flj11067
5d2ba0a1



98.2 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
6c1yz6A_



98.1 24 PDB header:translation
Chain: A: PDB Molecule:probable translation initiation factor 2 alpha
PDBTitle: crystal structure of intact alpha subunit of aif2 from2 pyrococcus abyssi
7d1q46a2



98.1 18 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
8c2z0sA_



98.1 14 PDB header:rna binding protein
Chain: A: PDB Molecule:probable exosome complex rna-binding protein 1;
PDBTitle: crystal structure of putative exosome complex rna-binding2 protein
9c2k4kA_



98.1 23 PDB header:rna binding protein
Chain: A: PDB Molecule:general stress protein 13;
PDBTitle: solution structure of gsp13 from bacillus subtilis
10d3bzka4



98.1 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
11c2je6I_



98.0 19 PDB header:hydrolase
Chain: I: PDB Molecule:exosome complex rna-binding protein 1;
PDBTitle: structure of a 9-subunit archaeal exosome
12c2khjA_



98.0 25 PDB header:ribosomal protein
Chain: A: PDB Molecule:30s ribosomal protein s1;
PDBTitle: nmr structure of the domain 6 of the e. coli ribosomal2 protein s1
13d2je6i1



98.0 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
14c2khiA_



98.0 14 PDB header:ribosomal protein
Chain: A: PDB Molecule:30s ribosomal protein s1;
PDBTitle: nmr structure of the domain 4 of the e. coli ribosomal2 protein s1
15c2ba0A_



97.9 16 PDB header:rna binding protein
Chain: A: PDB Molecule:archeal exosome rna binding protein rrp4;
PDBTitle: archaeal exosome core
16d2nn6h1



97.9 17 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
17c1q8kA_



97.9 19 PDB header:translation
Chain: A: PDB Molecule:eukaryotic translation initiation factor 2
PDBTitle: solution structure of alpha subunit of human eif2
18c2eqsA_



97.9 38 PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent rna helicase dhx8;
PDBTitle: solution structure of the s1 rna binding domain of human2 atp-dependent rna helicase dhx8
19d1wi5a_



97.9 22 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
20d1sroa_



97.9 32 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
21d1go3e1



not modelled 97.8 18 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
22c1q46A_



not modelled 97.8 19 PDB header:translation
Chain: A: PDB Molecule:translation initiation factor 2 alpha subunit;
PDBTitle: crystal structure of the eif2 alpha subunit from2 saccharomyces cerevisia
23d1hh2p1



not modelled 97.7 27 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
24c3go5A_



not modelled 97.6 12 PDB header:gene regulation
Chain: A: PDB Molecule:multidomain protein with s1 rna-binding domains;
PDBTitle: crystal structure of a multidomain protein with nucleic acid binding2 domains (sp_0946) from streptococcus pneumoniae tigr4 at 1.40 a3 resolution
25c2oceA_



not modelled 97.6 20 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein pa5201;
PDBTitle: crystal structure of tex family protein pa5201 from2 pseudomonas aeruginosa
26c1hh2P_



not modelled 97.6 26 PDB header:transcription regulation
Chain: P: PDB Molecule:n utilization substance protein a;
PDBTitle: crystal structure of nusa from thermotoga maritima
27c2ba1B_



not modelled 97.5 16 PDB header:rna binding protein
Chain: B: PDB Molecule:archaeal exosome rna binding protein csl4;
PDBTitle: archaeal exosome core
28c2ahoB_



not modelled 97.4 27 PDB header:translation
Chain: B: PDB Molecule:translation initiation factor 2 alpha subunit;
PDBTitle: structure of the archaeal initiation factor eif2 alpha-2 gamma heterodimer from sulfolobus solfataricus complexed3 with gdpnp
29d2ahob2



not modelled 97.4 25 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
30c1l2fA_



not modelled 97.4 27 PDB header:transcription
Chain: A: PDB Molecule:n utilization substance protein a;
PDBTitle: crystal structure of nusa from thermotoga maritima: a2 structure-based role of the n-terminal domain
31d2nn6i1



not modelled 97.4 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
32d1kl9a2



not modelled 97.3 18 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
33c2k52A_



not modelled 97.3 29 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein mj1198;
PDBTitle: structure of uncharacterized protein mj1198 from2 methanocaldococcus jannaschii. northeast structural3 genomics target mjr117b
34c1go3E_



not modelled 97.1 20 PDB header:transferase
Chain: E: PDB Molecule:dna-directed rna polymerase subunit e;
PDBTitle: structure of an archeal homolog of the eukaryotic rna2 polymerase ii rpb4/rpb7 complex
35c3psiA_



not modelled 97.1 13 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)
36c2nn6I_



not modelled 97.0 19 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
37d1y14b1



not modelled 97.0 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
38c2c35F_



not modelled 96.5 15 PDB header:polymerase
Chain: F: PDB Molecule:dna-directed rna polymerase ii 19 kda
PDBTitle: subunits rpb4 and rpb7 of human rna polymerase ii
39c3h0gS_



not modelled 96.5 12 PDB header:transcription
Chain: S: PDB Molecule:dna-directed rna polymerase ii subunit rpb7;
PDBTitle: rna polymerase ii from schizosaccharomyces pombe
40c1kl9A_



not modelled 96.4 21 PDB header:translation
Chain: A: PDB Molecule:eukaryotic translation initiation factor 2 subunit 1;
PDBTitle: crystal structure of the n-terminal segment of human eukaryotic2 initiation factor 2alpha
41d2nn6g1



not modelled 96.3 20 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
42c2b8kG_



not modelled 96.2 14 PDB header:transferase
Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kda
PDBTitle: 12-subunit rna polymerase ii
43d2c35b1



not modelled 95.6 18 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
44c2pmzE_



not modelled 95.4 16 PDB header:translation, transferase
Chain: E: PDB Molecule:dna-directed rna polymerase subunit e;
PDBTitle: archaeal rna polymerase from sulfolobus solfataricus
45c2bh8B_



not modelled 95.4 20 PDB header:transcription
Chain: B: PDB Molecule:1b11;
PDBTitle: combinatorial protein 1b11
46c1nt9G_



not modelled 95.3 14 PDB header:transcription, transferase
Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kd polypeptide;
PDBTitle: complete 12-subunit rna polymerase ii
47c3aqqD_



not modelled 95.1 25 PDB header:dna binding protein
Chain: D: PDB Molecule:calcium-regulated heat stable protein 1;
PDBTitle: crystal structure of human crhsp-24
48c2nn6H_



not modelled 94.7 15 PDB header:hydrolase/transferase
Chain: H: PDB Molecule:exosome complex exonuclease rrp4;
PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40
49c2ckzB_



not modelled 94.6 13 PDB header:transferase
Chain: B: PDB Molecule:dna-directed rna polymerase iii 25 kd
PDBTitle: x-ray structure of rna polymerase iii subcomplex c17-c25.
50d2asba1



not modelled 94.4 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
51c2nn6G_



not modelled 94.2 19 PDB header:hydrolase/transferase
Chain: G: PDB Molecule:exosome complex exonuclease rrp40;
PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40
52c1k0rB_



not modelled 94.0 20 PDB header:transcription
Chain: B: PDB Molecule:nusa;
PDBTitle: crystal structure of mycobacterium tuberculosis nusa
53c2asbA_



not modelled 94.0 23 PDB header:transcription/rna
Chain: A: PDB Molecule:transcription elongation protein nusa;
PDBTitle: structure of a mycobacterium tuberculosis nusa-rna complex
54d2ja9a1



not modelled 92.9 22 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
55d1c9oa_



not modelled 92.5 27 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
56d1h95a_



not modelled 91.3 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
57c2ljpA_



not modelled 90.8 10 PDB header:hydrolase
Chain: A: PDB Molecule:ribonuclease p protein component;
PDBTitle: backbone 1h, 13c, and 15n chemical shift assignments for e.coli2 ribonuclease p protein
58d1mjca_



not modelled 90.5 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
59d2es2a1



not modelled 90.5 27 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
60c2kcmA_



not modelled 88.7 19 PDB header:nucleic acid binding protein
Chain: A: PDB Molecule:cold shock domain family protein;
PDBTitle: solution nmr structure of the n-terminal ob-domain of so_1732 from2 shewanella oneidensis. northeast structural genomics consortium3 target sor210a.
61d1g6pa_



not modelled 88.3 24 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
62d1d6ta_



not modelled 87.7 21 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:RNase P protein
63d1nz0a_



not modelled 87.6 21 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:RNase P protein
64c2eqjA_



not modelled 86.9 19 PDB header:transcription
Chain: A: PDB Molecule:metal-response element-binding transcription
PDBTitle: solution structure of the tudor domain of metal-response2 element-binding transcription factor 2
65c2ja9A_



not modelled 86.2 14 PDB header:rna-binding protein
Chain: A: PDB Molecule:exosome complex exonuclease rrp40;
PDBTitle: structure of the n-terminal deletion of yeast exosome2 component rrp40
66d1k3ra1



not modelled 85.8 14 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Hypothetical protein MTH1 (MT0001), insert domain
67c2hnkC_



not modelled 85.6 20 PDB header:transferase
Chain: C: PDB Molecule:sam-dependent o-methyltransferase;
PDBTitle: crystal structure of sam-dependent o-methyltransferase from2 pathogenic bacterium leptospira interrogans
68c2wp8J_



not modelled 85.3 11 PDB header:hydrolase
Chain: J: PDB Molecule:exosome complex exonuclease dis3;
PDBTitle: yeast rrp44 nuclease
69c2e5pA_



not modelled 84.0 20 PDB header:transcription
Chain: A: PDB Molecule:phd finger protein 1;
PDBTitle: solution structure of the tudor domain of phd finger2 protein 1 (phf1 protein)
70c3d0fA_



not modelled 83.6 10 PDB header:transferase
Chain: A: PDB Molecule:penicillin-binding 1 transmembrane protein mrca;
PDBTitle: structure of the big_1156.2 domain of putative penicillin-binding2 protein mrca from nitrosomonas europaea atcc 19718
71c2k5nA_



not modelled 83.5 18 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative cold-shock protein;
PDBTitle: solution nmr structure of the n-terminal domain of protein2 eca1580 from erwinia carotovora, northeast structural3 genomics consortium target ewr156a
72c2pe4A_



not modelled 83.4 20 PDB header:hydrolase
Chain: A: PDB Molecule:hyaluronidase-1;
PDBTitle: structure of human hyaluronidase 1, a hyaluronan hydrolyzing enzyme2 involved in tumor growth and angiogenesis
73d1a6fa_



not modelled 82.7 16 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:RNase P protein
74c3trzE_



not modelled 81.5 25 PDB header:rna binding protein/rna
Chain: E: PDB Molecule:protein lin-28 homolog a;
PDBTitle: mouse lin28a in complex with let-7d microrna pre-element
75c3pihA_



not modelled 81.5 20 PDB header:hydrolase/dna
Chain: A: PDB Molecule:uvrabc system protein a;
PDBTitle: t. maritima uvra in complex with fluorescein-modified dna
76c3pnwX_



not modelled 81.0 23 PDB header:protein binding/immune system
Chain: X: PDB Molecule:tudor domain-containing protein 3;
PDBTitle: crystal structure of the tudor domain of human tdrd3 in complex with2 an anti-tdrd3 fab
77c2bx9J_



not modelled 79.8 36 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
78c3a0jB_



not modelled 78.1 17 PDB header:transcription
Chain: B: PDB Molecule:cold shock protein;
PDBTitle: crystal structure of cold shock protein 1 from thermus2 thermophilus hb8
79c2ytvA_



not modelled 77.2 20 PDB header:rna binding protein
Chain: A: PDB Molecule:cold shock domain-containing protein e1;
PDBTitle: solution structure of the fifth cold-shock domain of the human2 kiaa0885 protein (unr protein)
80c2e5qA_



not modelled 76.0 24 PDB header:transcription
Chain: A: PDB Molecule:phd finger protein 19;
PDBTitle: solution structure of the tudor domain of phd finger2 protein 19, isoform b [homo sapiens]
81c3ld0Q_



not modelled 75.1 30 PDB header:gene regulation
Chain: Q: PDB Molecule:inhibitor of trap, regulated by t-box (trp) sequence rtpa;
PDBTitle: crystal structure of b.licheniformis anti-trap protein, an antagonist2 of trap-rna interactions
82c2d9tA_



not modelled 73.8 23 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:tudor domain-containing protein 3;
PDBTitle: solution structure of the tudor domain of tudor domain2 containing protein 3 from mouse
83c2atmA_



not modelled 73.6 23 PDB header:hydrolase
Chain: A: PDB Molecule:hyaluronoglucosaminidase;
PDBTitle: crystal structure of the recombinant allergen ves v 2
84d1fcqa_



not modelled 72.4 25 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Bee venom hyaluronidase
85c1g5vA_



not modelled 70.2 19 PDB header:translation
Chain: A: PDB Molecule:survival motor neuron protein 1;
PDBTitle: solution structure of the tudor domain of the human smn2 protein
86d1mhna_



not modelled 70.0 19 Fold:SH3-like barrel
Superfamily:Tudor/PWWP/MBT
Family:Tudor domain
87c1fcuA_



not modelled 69.6 26 PDB header:hydrolase
Chain: A: PDB Molecule:hyaluronoglucosaminidase;
PDBTitle: crystal structure (trigonal) of bee venom hyaluronidase
88c3cbgA_



not modelled 68.7 28 PDB header:transferase
Chain: A: PDB Molecule:o-methyltransferase;
PDBTitle: functional and structural characterization of a2 cationdependent o-methyltransferase from the3 cyanobacterium synechocystis sp. strain pcc 6803
89d1nlta3



not modelled 67.9 28 Fold:DnaJ/Hsp40 cysteine-rich domain
Superfamily:DnaJ/Hsp40 cysteine-rich domain
Family:DnaJ/Hsp40 cysteine-rich domain
90c3camB_



not modelled 67.4 21 PDB header:gene regulation
Chain: B: PDB Molecule:cold-shock domain family protein;
PDBTitle: crystal structure of the cold shock domain protein from neisseria2 meningitidis
91c3ayhB_



not modelled 66.8 15 PDB header:transcription
Chain: B: PDB Molecule:dna-directed rna polymerase iii subunit rpc8;
PDBTitle: crystal structure of the c17/25 subcomplex from s. pombe rna2 polymerase iii
92c3tr6A_



not modelled 65.4 30 PDB header:transferase
Chain: A: PDB Molecule:o-methyltransferase;
PDBTitle: structure of a o-methyltransferase from coxiella burnetii
93d3d3ra1



not modelled 63.8 20 Fold:OB-fold
Superfamily:HupF/HypC-like
Family:HupF/HypC-like
94d1bi9a_



not modelled 63.2 19 Fold:ALDH-like
Superfamily:ALDH-like
Family:ALDH-like
95d2ix0a2



not modelled 62.6 24 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
96c3nthA_



not modelled 62.6 25 PDB header:transcription
Chain: A: PDB Molecule:maternal protein tudor;
PDBTitle: crystal structure of tudor and aubergine [r13(me2s)] complex
97c2hl7A_



not modelled 61.5 19 PDB header:oxidoreductase
Chain: A: PDB Molecule:cytochrome c-type biogenesis protein ccmh;
PDBTitle: crystal structure of the periplasmic domain of ccmh from pseudomonas2 aeruginosa
98d1wfqa_



not modelled 58.1 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
99c1nltA_



not modelled 57.8 21 PDB header:protein transport
Chain: A: PDB Molecule:mitochondrial protein import protein mas5;
PDBTitle: the crystal structure of hsp40 ydj1
100c1x65A_



not modelled 56.9 15 PDB header:rna binding protein
Chain: A: PDB Molecule:unr protein;
PDBTitle: solution structure of the third cold-shock domain of the human2 kiaa0885 protein (unr protein)
101c1tt9B_



not modelled 56.5 38 PDB header:transferase, lyase
Chain: B: PDB Molecule:formimidoyltransferase-cyclodeaminase
PDBTitle: structure of the bifunctional and golgi associated2 formiminotransferase cyclodeaminase octamer
102c2hqxB_



not modelled 56.2 21 PDB header:transcription
Chain: B: PDB Molecule:p100 co-activator tudor domain;
PDBTitle: crystal structure of human p100 tudor domain conserved2 region
103d2hqxa1



not modelled 56.2 21 Fold:SH3-like barrel
Superfamily:Tudor/PWWP/MBT
Family:Tudor domain
104c3d3rA_



not modelled 55.4 20 PDB header:chaperone
Chain: A: PDB Molecule:hydrogenase assembly chaperone hypc/hupf;
PDBTitle: crystal structure of the hydrogenase assembly chaperone hypc/hupf2 family protein from shewanella oneidensis mr-1
105c2ix1A_



not modelled 55.4 16 PDB header:hydrolase
Chain: A: PDB Molecule:exoribonuclease 2;
PDBTitle: rnase ii d209n mutant
106d1h9ma1



not modelled 54.5 19 Fold:OB-fold
Superfamily:MOP-like
Family:BiMOP, duplicated molybdate-binding domain
107d1vlua_



not modelled 54.4 18 Fold:ALDH-like
Superfamily:ALDH-like
Family:ALDH-like
108d1a62a2



not modelled 53.4 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
109d1h9ra1



not modelled 52.8 26 Fold:OB-fold
Superfamily:MOP-like
Family:BiMOP, duplicated molybdate-binding domain
110c2cttA_



not modelled 52.7 31 PDB header:chaperone
Chain: A: PDB Molecule:dnaj homolog subfamily a member 3;
PDBTitle: solution structure of zinc finger domain from human dnaj2 subfamily a menber 3
111c3bdlA_



not modelled 52.6 21 PDB header:hydrolase
Chain: A: PDB Molecule:staphylococcal nuclease domain-containing
PDBTitle: crystal structure of a truncated human tudor-sn
112d2d9ta1



not modelled 52.1 26 Fold:SH3-like barrel
Superfamily:Tudor/PWWP/MBT
Family:Tudor domain
113d1exka_



not modelled 50.9 38 Fold:DnaJ/Hsp40 cysteine-rich domain
Superfamily:DnaJ/Hsp40 cysteine-rich domain
Family:DnaJ/Hsp40 cysteine-rich domain
114d1p6oa_



not modelled 50.1 14 Fold:Cytidine deaminase-like
Superfamily:Cytidine deaminase-like
Family:Deoxycytidylate deaminase-like
115c3lz8A_



not modelled 49.8 20 PDB header:chaperone
Chain: A: PDB Molecule:putative chaperone dnaj;
PDBTitle: structure of a putative chaperone dnaj from klebsiella pneumoniae2 subsp. pneumoniae mgh 78578 at 2.9 a resolution.
116c4a4fA_



not modelled 49.5 26 PDB header:rna binding protein
Chain: A: PDB Molecule:survival of motor neuron-related-splicing factor 30;
PDBTitle: solution structure of spf30 tudor domain in complex with2 symmetrically dimethylated arginine
117c2ytxA_



not modelled 49.3 15 PDB header:rna binding protein
Chain: A: PDB Molecule:cold shock domain-containing protein e1;
PDBTitle: solution structure of the second cold-shock domain of the human2 kiaa0885 protein (unr protein)
118d1guta_



not modelled 49.2 17 Fold:OB-fold
Superfamily:MOP-like
Family:Molybdate/tungstate binding protein MOP
119c2eqkA_



not modelled 49.2 25 PDB header:transcription
Chain: A: PDB Molecule:tudor domain-containing protein 4;
PDBTitle: solution structure of the tudor domain of tudor domain-2 containing protein 4
120d2diqa1



not modelled 46.8 25 Fold:SH3-like barrel
Superfamily:Tudor/PWWP/MBT
Family:Tudor domain

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