Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP21499
DateThu Jan 5 11:38:21 GMT 2012
Unique Job ID59084e3b54a2c37d

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c2ix1A_
Top template information
PDB header:hydrolase
Chain: A: PDB Molecule:exoribonuclease 2;
PDBTitle: rnase ii d209n mutant
Confidence and coverage
Confidence:100.0% Coverage: 77%
625 residues ( 77% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
739 residues ( 91%) could be modelled at >90% confidence using multiple-templates.
You may wish to try resubmitting your sequence in "intensive" mode to model more of your sequence.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

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












??
??








???











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

?




































???

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









































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   .........190.........200.........210.........220.........230.........240
Sequence  DQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQA
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Disorder 
??????




















































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   .........250.........260.........270.........280.........290.........300
Sequence  VEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIA
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?
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   .........310.........320.........330.........340.........350.........360
Sequence  DVSYYVRPSTPLDREARNRGTSVYFPSQVIPMLPEVLSNGLCSLNPQVDRLCMVCEMTVS
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   .........370.........380.........390.........400.........410.........420
Sequence  SKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQYAPLVKHLEELHNLYKVLDKA
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?????





















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   .........430.........440.........450.........460.........470.........480
Sequence  REERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEP
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?





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   .........490.........500.........510.........520.........530.........540
Sequence  ALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLL
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?????

























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   .........550.........560.........570.........580.........590.........600
Sequence  RSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLTLHRAIKYLLAKEQGHQGNTTETG
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Disorder 
??????????





































???????????
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   .........610.........620.........630.........640.........650.........660
Sequence  GYHYSMEEMLQLGQHCSMAERRADEATRDVADWLKCDFMLDQVGNVFKGVISSVTGFGFF
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Disorder  ????























































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   .........670.........680.........690.........700.........710.........720
Sequence  VRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLMGESSGQTYRLGDRVEVRVEAVNMDERKI
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   .........730.........740.........750.........760.........770.........780
Sequence  DFSLISSERAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKTKPKAA
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Disorder 




???????????????????????????????????????????????????????
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   .........790.........800.........810...
Sequence  KKDARKAKKPSAKTQKIAAATKAKRAAKKKVAE
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SS confidence 
































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 2ix1 chain A

3D model

Region: 75 - 725
Aligned: 625
Modelled: 637
Confidence: 100.0%
Identity: 25%
PDB header:hydrolase
Chain: A: PDB Molecule:exoribonuclease 2;
PDBTitle: rnase ii d209n mutant

Phyre2

PDB 2wp8 chain J

3D model

Region: 80 - 725
Aligned: 628
Modelled: 646
Confidence: 100.0%
Identity: 26%
PDB header:hydrolase
Chain: J: PDB Molecule:exosome complex exonuclease dis3;
PDBTitle: yeast rrp44 nuclease

Phyre2

PDB 2vnu chain D

3D model

Region: 56 - 716
Aligned: 628
Modelled: 645
Confidence: 100.0%
Identity: 25%
PDB header:hydrolase/rna
Chain: D: PDB Molecule:exosome complex exonuclease rrp44;
PDBTitle: crystal structure of sc rrp44

Phyre2

PDB 2r7f chain A

3D model

Region: 184 - 725
Aligned: 453
Modelled: 460
Confidence: 100.0%
Identity: 24%
PDB header:hydrolase
Chain: A: PDB Molecule:ribonuclease ii family protein;
PDBTitle: crystal structure of ribonuclease ii family protein from2 deinococcus radiodurans, hexagonal crystal form. northeast3 structural genomics target drr63

Phyre2

PDB 2r7d chain A domain 2

3D model

Region: 184 - 642
Aligned: 395
Modelled: 421
Confidence: 100.0%
Identity: 26%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: RNB domain-like

Phyre2

PDB 2ix0 chain A domain 4

3D model

Region: 247 - 642
Aligned: 381
Modelled: 382
Confidence: 100.0%
Identity: 28%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: RNB domain-like

Phyre2

PDB 2vnu chain D domain 4

3D model

Region: 223 - 641
Aligned: 401
Modelled: 419
Confidence: 100.0%
Identity: 27%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: RNB domain-like

Phyre2

PDB 2ix0 chain A domain 1

3D model

Region: 150 - 233
Aligned: 84
Modelled: 84
Confidence: 99.7%
Identity: 15%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 1go3 chain E domain 1

3D model

Region: 642 - 731
Aligned: 86
Modelled: 90
Confidence: 99.6%
Identity: 30%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 3h0g chain S

3D model

Region: 562 - 720
Aligned: 144
Modelled: 159
Confidence: 99.6%
Identity: 16%
PDB header:transcription
Chain: S: PDB Molecule:dna-directed rna polymerase ii subunit rpb7;
PDBTitle: rna polymerase ii from schizosaccharomyces pombe

Phyre2

PDB 2c35 chain B domain 1

3D model

Region: 640 - 720
Aligned: 79
Modelled: 81
Confidence: 99.6%
Identity: 13%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2vnu chain D domain 1

3D model

Region: 149 - 236
Aligned: 86
Modelled: 88
Confidence: 99.5%
Identity: 21%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2ix0 chain A domain 2

3D model

Region: 75 - 143
Aligned: 65
Modelled: 69
Confidence: 99.4%
Identity: 25%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2b8k chain G

3D model

Region: 634 - 724
Aligned: 88
Modelled: 89
Confidence: 99.4%
Identity: 18%
PDB header:transferase
Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kda
PDBTitle: 12-subunit rna polymerase ii

Phyre2

PDB 2c35 chain F

3D model

Region: 636 - 723
Aligned: 86
Modelled: 88
Confidence: 99.4%
Identity: 12%
PDB header:polymerase
Chain: F: PDB Molecule:dna-directed rna polymerase ii 19 kda
PDBTitle: subunits rpb4 and rpb7 of human rna polymerase ii

Phyre2

PDB 1go3 chain E

3D model

Region: 639 - 731
Aligned: 89
Modelled: 93
Confidence: 99.3%
Identity: 29%
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

Phyre2

PDB 2k52 chain A

3D model

Region: 639 - 728
Aligned: 74
Modelled: 75
Confidence: 99.2%
Identity: 27%
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

Phyre2

PDB 1y14 chain B domain 1

3D model

Region: 642 - 720
Aligned: 71
Modelled: 79
Confidence: 99.2%
Identity: 23%
Fold: OB-fold
Superfamily: Nucleic acid-binding proteins
Family: Cold shock DNA-binding domain-like

Phyre2

PDB 2pmz chain E

3D model

Region: 639 - 731
Aligned: 91
Modelled: 93
Confidence: 99.2%
Identity: 30%
PDB header:translation, transferase
Chain: E: PDB Molecule:dna-directed rna polymerase subunit e;
PDBTitle: archaeal rna polymerase from sulfolobus solfataricus

Phyre2

PDB 2vnu chain D domain 3

3D model

Region: 83 - 148
Aligned: 66
Modelled: 66
Confidence: 99.2%
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: 643 - 749
Aligned: 96
Modelled: 96
Confidence: 99.1%
Identity: 20%
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 3k2z chain A

3D model

Region: 22 - 183
Aligned: 152
Modelled: 152
Confidence: 98.0%
Identity: 20%
PDB header:hydrolase
Chain: A: PDB Molecule:lexa repressor;
PDBTitle: crystal structure of a lexa protein from thermotoga maritima

Phyre2

PDB 1mkm chain A domain 1

3D model

Region: 23 - 78
Aligned: 52
Modelled: 52
Confidence: 96.7%
Identity: 17%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: Transcriptional regulator IclR, N-terminal domain

Phyre2

PDB 1mkm chain A

3D model

Region: 23 - 79
Aligned: 53
Modelled: 53
Confidence: 96.5%
Identity: 17%
PDB header:transcription
Chain: A: PDB Molecule:iclr transcriptional regulator;
PDBTitle: crystal structure of the thermotoga maritima iclr

Phyre2

PDB 2o0y chain B

3D model

Region: 23 - 82
Aligned: 56
Modelled: 54
Confidence: 95.0%
Identity: 16%
PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator rha1_ro069532 (iclr-family) from rhodococcus sp.

Phyre2

PDB 3bro chain A domain 1

3D model

Region: 6 - 73
Aligned: 63
Modelled: 61
Confidence: 90.5%
Identity: 19%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: MarR-like transcriptional regulators

Phyre2
1

c2ix1A_
2

c2wp8J_
3

c2vnuD_
4

c2r7fA_
5

d2r7da2
6

d2ix0a4
7

d2vnud4
8

d2ix0a1
9

d1go3e1
10

c3h0gS_
11

d2c35b1
12

d2vnud1
13

d2ix0a2
14

c2b8kG_
15

c2c35F_
16

c1go3E_
17

c2k52A_
18

d1y14b1
19

c2pmzE_
20

d2vnud3
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c2cqoA_
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c3k2zA_
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d1mkma1
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c1mkmA_
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c2o0yB_
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d3broa1
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2ix1A_



100.0 25 PDB header:hydrolase
Chain: A: PDB Molecule:exoribonuclease 2;
PDBTitle: rnase ii d209n mutant
2c2wp8J_



100.0 26 PDB header:hydrolase
Chain: J: PDB Molecule:exosome complex exonuclease dis3;
PDBTitle: yeast rrp44 nuclease
3c2vnuD_



100.0 25 PDB header:hydrolase/rna
Chain: D: PDB Molecule:exosome complex exonuclease rrp44;
PDBTitle: crystal structure of sc rrp44
4c2r7fA_



100.0 24 PDB header:hydrolase
Chain: A: PDB Molecule:ribonuclease ii family protein;
PDBTitle: crystal structure of ribonuclease ii family protein from2 deinococcus radiodurans, hexagonal crystal form. northeast3 structural genomics target drr63
5d2r7da2



100.0 26 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:RNB domain-like
6d2ix0a4



100.0 28 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:RNB domain-like
7d2vnud4



100.0 27 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:RNB domain-like
8d2ix0a1



99.7 15 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
9d1go3e1



99.6 30 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
10c3h0gS_



99.6 16 PDB header:transcription
Chain: S: PDB Molecule:dna-directed rna polymerase ii subunit rpb7;
PDBTitle: rna polymerase ii from schizosaccharomyces pombe
11d2c35b1



99.6 13 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
12d2vnud1



99.5 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
13d2ix0a2



99.4 25 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
14c2b8kG_



99.4 18 PDB header:transferase
Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kda
PDBTitle: 12-subunit rna polymerase ii
15c2c35F_



99.4 12 PDB header:polymerase
Chain: F: PDB Molecule:dna-directed rna polymerase ii 19 kda
PDBTitle: subunits rpb4 and rpb7 of human rna polymerase ii
16c1go3E_



99.3 29 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
17c2k52A_



99.2 27 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
18d1y14b1



99.2 23 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
19c2pmzE_



99.2 30 PDB header:translation, transferase
Chain: E: PDB Molecule:dna-directed rna polymerase subunit e;
PDBTitle: archaeal rna polymerase from sulfolobus solfataricus
20d2vnud3



99.2 15 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
21c1nt9G_



not modelled 99.2 20 PDB header:transcription, transferase
Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kd polypeptide;
PDBTitle: complete 12-subunit rna polymerase ii
22d1kl9a2



not modelled 99.2 32 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
23c2ckzB_



not modelled 99.1 15 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.
24c2cqoA_



99.1 20 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
25d1q46a2



not modelled 99.1 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
26c1yz6A_



not modelled 99.1 22 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
27c1q46A_



not modelled 99.1 21 PDB header:translation
Chain: A: PDB Molecule:translation initiation factor 2 alpha subunit;
PDBTitle: crystal structure of the eif2 alpha subunit from2 saccharomyces cerevisia
28c2khiA_



not modelled 99.0 29 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
29c2khjA_



not modelled 99.0 26 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
30c2k4kA_



not modelled 98.9 35 PDB header:rna binding protein
Chain: A: PDB Molecule:general stress protein 13;
PDBTitle: solution structure of gsp13 from bacillus subtilis
31c2eqsA_



not modelled 98.9 27 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
32c1q8kA_



not modelled 98.9 31 PDB header:translation
Chain: A: PDB Molecule:eukaryotic translation initiation factor 2
PDBTitle: solution structure of alpha subunit of human eif2
33c2oceA_



not modelled 98.9 33 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein pa5201;
PDBTitle: crystal structure of tex family protein pa5201 from2 pseudomonas aeruginosa
34d3bzka4



not modelled 98.9 33 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
35c3psiA_



not modelled 98.8 12 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)
36c2ahoB_



not modelled 98.8 22 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
37c1kl9A_



not modelled 98.8 30 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
38d1sroa_



not modelled 98.7 31 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
39d2z0sa1



not modelled 98.7 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
40d2ba0a1



not modelled 98.7 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
41d2je6i1



not modelled 98.7 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
42d2ahob2



not modelled 98.6 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
43d1wi5a_



not modelled 98.6 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
44c1l2fA_



not modelled 98.6 14 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
45c3go5A_



not modelled 98.6 25 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
46c1hh2P_



not modelled 98.4 14 PDB header:transcription regulation
Chain: P: PDB Molecule:n utilization substance protein a;
PDBTitle: crystal structure of nusa from thermotoga maritima
47d1hh2p1



not modelled 98.4 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
48d2nn6h1



not modelled 98.3 23 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
49c3ayhB_



not modelled 98.2 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
50c2z0sA_



not modelled 98.2 19 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
51c3k2zA_



98.0 20 PDB header:hydrolase
Chain: A: PDB Molecule:lexa repressor;
PDBTitle: crystal structure of a lexa protein from thermotoga maritima
52c2bh8B_



not modelled 97.8 51 PDB header:transcription
Chain: B: PDB Molecule:1b11;
PDBTitle: combinatorial protein 1b11
53d2ix0a3



not modelled 97.7 20 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
54d2vnud2



not modelled 97.7 26 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
55c2ba0A_



not modelled 97.7 19 PDB header:rna binding protein
Chain: A: PDB Molecule:archeal exosome rna binding protein rrp4;
PDBTitle: archaeal exosome core
56d1smxa_



not modelled 97.7 18 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
57d2nn6i1



not modelled 97.6 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
58c3aqqD_



not modelled 97.4 18 PDB header:dna binding protein
Chain: D: PDB Molecule:calcium-regulated heat stable protein 1;
PDBTitle: crystal structure of human crhsp-24
59c2a8vA_



not modelled 97.3 24 PDB header:protein/rna
Chain: A: PDB Molecule:rna binding domain of rho transcription
PDBTitle: rho transcription termination factor/rna complex
60c2je6I_



not modelled 97.2 17 PDB header:hydrolase
Chain: I: PDB Molecule:exosome complex rna-binding protein 1;
PDBTitle: structure of a 9-subunit archaeal exosome
61c2nn6I_



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
62c2rf4A_



not modelled 97.0 16 PDB header:transferase
Chain: A: PDB Molecule:dna-directed rna polymerase i subunit rpa4;
PDBTitle: crystal structure of the rna polymerase i subcomplex a14/43
63c3a0jB_



not modelled 96.9 26 PDB header:transcription
Chain: B: PDB Molecule:cold shock protein;
PDBTitle: crystal structure of cold shock protein 1 from thermus2 thermophilus hb8
64d1a62a2



not modelled 96.9 28 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
65d1mjca_



not modelled 96.9 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
66c2ytxA_



not modelled 96.8 24 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)
67d1g6pa_



not modelled 96.8 22 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
68d1wfqa_



not modelled 96.7 22 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
69d1mkma1



96.7 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Transcriptional regulator IclR, N-terminal domain
70c2ytyA_



not modelled 96.6 17 PDB header:rna binding protein
Chain: A: PDB Molecule:cold shock domain-containing protein e1;
PDBTitle: solution structure of the fourth cold-shock domain of the human2 kiaa0885 protein (unr protein)
71d1h95a_



not modelled 96.6 25 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
72c2ba1B_



not modelled 96.6 20 PDB header:rna binding protein
Chain: B: PDB Molecule:archaeal exosome rna binding protein csl4;
PDBTitle: archaeal exosome core
73c1mkmA_



96.5 17 PDB header:transcription
Chain: A: PDB Molecule:iclr transcriptional regulator;
PDBTitle: crystal structure of the thermotoga maritima iclr
74c3camB_



not modelled 96.5 23 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
75c2k5nA_



not modelled 96.3 22 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
76c2xroE_



not modelled 95.9 15 PDB header:dna-binding protein/dna
Chain: E: PDB Molecule:hth-type transcriptional regulator ttgv;
PDBTitle: crystal structure of ttgv in complex with its dna operator
77d1jhfa1



not modelled 95.9 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:LexA repressor, N-terminal DNA-binding domain
78c1j5yA_



not modelled 95.9 19 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, biotin repressor family;
PDBTitle: crystal structure of transcriptional regulator (tm1602) from2 thermotoga maritima at 2.3 a resolution
79c3mq0A_



not modelled 95.8 16 PDB header:transcription repressor
Chain: A: PDB Molecule:transcriptional repressor of the blcabc operon;
PDBTitle: crystal structure of agobacterium tumefaciens repressor blcr
80c3hruA_



not modelled 95.6 15 PDB header:transcription
Chain: A: PDB Molecule:metalloregulator scar;
PDBTitle: crystal structure of scar with bound zn2+
81d2es2a1



not modelled 95.5 24 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
82c2kcmA_



not modelled 95.4 21 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.
83c1x65A_



not modelled 95.2 18 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)
84d1c9oa_



not modelled 95.2 25 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
85d1biaa1



not modelled 95.1 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
86c2o0yB_



95.0 16 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator rha1_ro069532 (iclr-family) from rhodococcus sp.
87d1j5ya1



not modelled 95.0 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
88c1uwvA_



not modelled 94.9 16 PDB header:transferase
Chain: A: PDB Molecule:23s rrna (uracil-5-)-methyltransferase ruma;
PDBTitle: crystal structure of ruma, the iron-sulfur cluster2 containing e. coli 23s ribosomal rna 5-methyluridine3 methyltransferase
89d1xmka1



not modelled 94.8 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Z-DNA binding domain
90c2g7uB_



not modelled 94.8 20 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: 2.3 a structure of putative catechol degradative operon regulator from2 rhodococcus sp. rha1
91d1uwva1



not modelled 94.8 15 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:TRAM domain
92d1stza1



not modelled 94.6 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Heat-inducible transcription repressor HrcA, N-terminal domain
93d2p4wa1



not modelled 94.5 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:PF1790-like
94d2nn6g1



not modelled 94.4 15 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
95c1z6rC_



not modelled 94.3 10 PDB header:transcription
Chain: C: PDB Molecule:mlc protein;
PDBTitle: crystal structure of mlc from escherichia coli
96d2d1ha1



not modelled 94.3 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
97c2it0A_



not modelled 94.1 24 PDB header:transcription/dna
Chain: A: PDB Molecule:iron-dependent repressor ider;
PDBTitle: crystal structure of a two-domain ider-dna complex crystal2 form ii
98d2hr3a1



not modelled 94.0 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
99c1f5tA_



not modelled 94.0 21 PDB header:transcription/dna
Chain: A: PDB Molecule:diphtheria toxin repressor;
PDBTitle: diphtheria tox repressor (c102d mutant) complexed with2 nickel and dtxr consensus binding sequence
100c3trzE_



not modelled 93.9 19 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
101c2ytvA_



not modelled 93.9 23 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)
102d1z05a1



not modelled 93.8 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ROK associated domain
103d1luza_



not modelled 93.7 20 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
104c2oqgA_



not modelled 93.7 24 PDB header:transcription
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein;
PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1
105d1lvaa3



not modelled 93.3 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:C-terminal fragment of elongation factor SelB
106c3r4kD_



not modelled 93.3 14 PDB header:dna binding protein
Chain: D: PDB Molecule:transcriptional regulator, iclr family;
PDBTitle: crystal structure of a putative iclr transcriptional regulator2 (tm1040_3717) from silicibacter sp. tm1040 at 2.46 a resolution
107c1k0rB_



not modelled 93.1 26 PDB header:transcription
Chain: B: PDB Molecule:nusa;
PDBTitle: crystal structure of mycobacterium tuberculosis nusa
108c3pqkD_



not modelled 93.0 26 PDB header:transcription
Chain: D: PDB Molecule:biofilm growth-associated repressor;
PDBTitle: crystal structure of the transcriptional repressor bigr from xylella2 fastidiosa
109c3f6vA_



not modelled 92.9 17 PDB header:transcription regulator
Chain: A: PDB Molecule:possible transcriptional regulator, arsr family
PDBTitle: crystal structure of possible transcriptional regulator for2 arsenical resistance
110d2htja1



not modelled 92.8 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:FaeA-like
111c1wsuA_



not modelled 92.8 21 PDB header:translation/rna
Chain: A: PDB Molecule:selenocysteine-specific elongation factor;
PDBTitle: c-terminal domain of elongation factor selb complexed with2 secis rna
112c1fx7C_



not modelled 92.7 25 PDB header:signaling protein
Chain: C: PDB Molecule:iron-dependent repressor ider;
PDBTitle: crystal structure of the iron-dependent regulator (ider)2 from mycobacterium tuberculosis
113c2h09A_



not modelled 92.6 15 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator mntr;
PDBTitle: crystal structure of diphtheria toxin repressor like protein2 from e. coli
114d1r1ua_



not modelled 92.6 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ArsR-like transcriptional regulators
115d1ku9a_



not modelled 92.4 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:DNA-binding protein Mj223
116c2ewnA_



not modelled 92.4 18 PDB header:ligase, transcription
Chain: A: PDB Molecule:bira bifunctional protein;
PDBTitle: ecoli biotin repressor with co-repressor analog
117c1r22B_



not modelled 92.2 17 PDB header:transcription repressor
Chain: B: PDB Molecule:transcriptional repressor smtb;
PDBTitle: crystal structure of the cyanobacterial metallothionein2 repressor smtb (c14s/c61s/c121s mutant) in the zn2alpha5-3 form
118c3cuoB_



not modelled 92.0 24 PDB header:transcription regulator
Chain: B: PDB Molecule:uncharacterized hth-type transcriptional regulator ygav;
PDBTitle: crystal structure of the predicted dna-binding transcriptional2 regulator from e. coli
119c3b73A_



not modelled 91.9 22 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:phih1 repressor-like protein;
PDBTitle: crystal structure of the phih1 repressor-like protein from2 haloarcula marismortui
120c2fe3B_



not modelled 91.9 20 PDB header:dna binding protein
Chain: B: PDB Molecule:peroxide operon regulator;
PDBTitle: the crystal structure of bacillus subtilis perr-zn reveals a novel2 zn(cys)4 structural redox switch

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