Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP05055
DateThu Jan 5 10:58:40 GMT 2012
Unique Job IDca1ca738bc4b240a

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1e3hA_
Top template information
PDB header:polyribonucleotide transferase
Chain: A: PDB Molecule:guanosine pentaphosphate synthetase;
PDBTitle: semet derivative of streptomyces antibioticus pnpase/gpsi2 enzyme
Confidence and coverage
Confidence:100.0% Coverage: 80%
569 residues ( 80% 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.
709 residues (100%) 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  MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT
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Disorder  ????







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???????






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
































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   .........130.........140.........150.........160.........170.........180
Sequence  NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA
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   .........190.........200.........210.........220.........230.........240
Sequence  GTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE
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?????










































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   .........250.........260.........270.........280.........290.........300
Sequence  ALNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLLAEDETLDENELGEILHAI
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   .........310.........320.........330.........340.........350.........360
Sequence  EKNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTAR
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??
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   .........370.........380.........390.........400.........410.........420
Sequence  DAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDK
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Disorder  ??????????















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???

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   .........430.........440.........450.........460.........470.........480
Sequence  FPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNYVVLSD
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   .........490.........500.........510.........520.........530.........540
Sequence  ILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQA
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   .........550.........560.........570.........580.........590.........600
Sequence  INAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTTIEIEDDGTVKIAAT
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??
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   .........610.........620.........630.........640.........650.........660
Sequence  DGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVE
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   .........670.........680.........690.........700.........710.
Sequence  KVTDYLQMGQEVPVKVLEVDRQGRIRLSIKEATEQSQPAAAPEAPAAEQGE
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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 1e3h chain A

3D model

Region: 3 - 573
Aligned: 569
Modelled: 570
Confidence: 100.0%
Identity: 45%
PDB header:polyribonucleotide transferase
Chain: A: PDB Molecule:guanosine pentaphosphate synthetase;
PDBTitle: semet derivative of streptomyces antibioticus pnpase/gpsi2 enzyme

Phyre2

PDB 3cdi chain A

3D model

Region: 2 - 542
Aligned: 516
Modelled: 528
Confidence: 100.0%
Identity: 100%
PDB header:transferase
Chain: A: PDB Molecule:polynucleotide phosphorylase;
PDBTitle: crystal structure of e. coli pnpase

Phyre2

PDB 3cdj chain A

3D model

Region: 1 - 540
Aligned: 442
Modelled: 469
Confidence: 100.0%
Identity: 100%
PDB header:transferase
Chain: A: PDB Molecule:polynucleotide phosphorylase;
PDBTitle: crystal structure of the e. coli kh/s1 domain truncated2 pnpase

Phyre2

PDB 2po2 chain A

3D model

Region: 307 - 550
Aligned: 232
Modelled: 244
Confidence: 100.0%
Identity: 28%
PDB header:hydrolase/hydrolase
Chain: A: PDB Molecule:probable exosome complex exonuclease 1;
PDBTitle: crystal structure of the p. abyssi exosome rnase ph ring2 complexed with cdp

Phyre2

PDB 2wnr chain B

3D model

Region: 314 - 543
Aligned: 218
Modelled: 230
Confidence: 100.0%
Identity: 31%
PDB header:hydrolase
Chain: B: PDB Molecule:probable exosome complex exonuclease 1;
PDBTitle: the structure of methanothermobacter thermautotrophicus2 exosome core assembly

Phyre2

PDB 2nn6 chain B

3D model

Region: 309 - 549
Aligned: 231
Modelled: 241
Confidence: 100.0%
Identity: 22%
PDB header:hydrolase/transferase
Chain: B: PDB Molecule:exosome complex exonuclease rrp41;
PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40

Phyre2

PDB 2ba1 chain D

3D model

Region: 307 - 550
Aligned: 235
Modelled: 243
Confidence: 100.0%
Identity: 26%
PDB header:rna binding protein
Chain: D: PDB Molecule:archaeal exosome complex exonuclease rrp41;
PDBTitle: archaeal exosome core

Phyre2

PDB 2c37 chain L

3D model

Region: 306 - 550
Aligned: 233
Modelled: 245
Confidence: 100.0%
Identity: 27%
PDB header:hydrolase
Chain: L: PDB Molecule:probable exosome complex exonuclease 1;
PDBTitle: rnase ph core of the archaeal exosome in complex with u82 rna

Phyre2

PDB 3dd6 chain A

3D model

Region: 314 - 548
Aligned: 228
Modelled: 235
Confidence: 100.0%
Identity: 25%
PDB header:transferase
Chain: A: PDB Molecule:ribonuclease ph;
PDBTitle: crystal structure of rph, an exoribonuclease from bacillus2 anthracis at 1.7 a resolution

Phyre2

PDB 2wp8 chain B

3D model

Region: 307 - 543
Aligned: 207
Modelled: 234
Confidence: 100.0%
Identity: 20%
PDB header:hydrolase
Chain: B: PDB Molecule:exosome complex component ski6;
PDBTitle: yeast rrp44 nuclease

Phyre2

PDB 1uds chain A

3D model

Region: 315 - 541
Aligned: 219
Modelled: 227
Confidence: 100.0%
Identity: 24%
PDB header:transferase
Chain: A: PDB Molecule:ribonuclease ph;
PDBTitle: crystal structure of the trna processing enzyme rnase ph r126a mutant2 from aquifex aeolicus

Phyre2

PDB 2pnz chain B

3D model

Region: 300 - 546
Aligned: 235
Modelled: 242
Confidence: 100.0%
Identity: 20%
PDB header:hydrolase/hydrolase
Chain: B: PDB Molecule:probable exosome complex exonuclease 2;
PDBTitle: crystal structure of the p. abyssi exosome rnase ph ring2 complexed with udp and gmp

Phyre2

PDB 3b4t chain C

3D model

Region: 314 - 544
Aligned: 217
Modelled: 223
Confidence: 100.0%
Identity: 24%
PDB header:transferase
Chain: C: PDB Molecule:ribonuclease ph;
PDBTitle: crystal structure of mycobacterium tuberculosis rnase ph, the2 mycobacterium tuberculosis structural genomics consortium target3 rv1340

Phyre2

PDB 1r6m chain A

3D model

Region: 314 - 543
Aligned: 218
Modelled: 220
Confidence: 100.0%
Identity: 25%
PDB header:transferase
Chain: A: PDB Molecule:ribonuclease ph;
PDBTitle: crystal structure of the trna processing enzyme rnase ph from2 pseudomonas aeruginosa in complex with phosphate

Phyre2

PDB 1e3h chain A domain 2

3D model

Region: 3 - 144
Aligned: 142
Modelled: 142
Confidence: 100.0%
Identity: 49%
Fold: Ribosomal protein S5 domain 2-like
Superfamily: Ribosomal protein S5 domain 2-like
Family: Ribonuclease PH domain 1-like

Phyre2

PDB 2nn6 chain C

3D model

Region: 307 - 543
Aligned: 227
Modelled: 237
Confidence: 100.0%
Identity: 18%
PDB header:hydrolase/transferase
Chain: C: PDB Molecule:exosome complex exonuclease rrp43;
PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40

Phyre2

PDB 2wnr chain C

3D model

Region: 310 - 542
Aligned: 221
Modelled: 229
Confidence: 100.0%
Identity: 18%
PDB header:hydrolase
Chain: C: PDB Molecule:probable exosome complex exonuclease 2;
PDBTitle: the structure of methanothermobacter thermautotrophicus2 exosome core assembly

Phyre2

PDB 3hkm chain B

3D model

Region: 315 - 543
Aligned: 208
Modelled: 229
Confidence: 100.0%
Identity: 23%
PDB header:hydrolase
Chain: B: PDB Molecule:os03g0854200 protein;
PDBTitle: crystal structure of rice(oryza sativa) rrp46

Phyre2

PDB 2ba0 chain I

3D model

Region: 295 - 538
Aligned: 230
Modelled: 244
Confidence: 100.0%
Identity: 22%
PDB header:rna binding protein
Chain: I: PDB Molecule:archeal exosome rna binding protein rrp42;
PDBTitle: archaeal exosome core

Phyre2

PDB 2nn6 chain E

3D model

Region: 301 - 545
Aligned: 237
Modelled: 244
Confidence: 100.0%
Identity: 17%
PDB header:hydrolase/transferase
Chain: E: PDB Molecule:exosome complex exonuclease rrp42;
PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40

Phyre2

PDB 2cqo chain A

3D model

Region: 615 - 711
Aligned: 97
Modelled: 97
Confidence: 99.6%
Identity: 27%
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 1q46 chain A

3D model

Region: 619 - 696
Aligned: 78
Modelled: 78
Confidence: 99.6%
Identity: 24%
PDB header:translation
Chain: A: PDB Molecule:translation initiation factor 2 alpha subunit;
PDBTitle: crystal structure of the eif2 alpha subunit from2 saccharomyces cerevisia

Phyre2

PDB 1yz6 chain A

3D model

Region: 619 - 696
Aligned: 78
Modelled: 78
Confidence: 99.6%
Identity: 42%
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 2k4k chain A

3D model

Region: 615 - 710
Aligned: 96
Modelled: 96
Confidence: 99.5%
Identity: 40%
PDB header:rna binding protein
Chain: A: PDB Molecule:general stress protein 13;
PDBTitle: solution structure of gsp13 from bacillus subtilis

Phyre2

PDB 2eqs chain A

3D model

Region: 618 - 706
Aligned: 88
Modelled: 88
Confidence: 99.5%
Identity: 33%
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 2khj chain A

3D model

Region: 613 - 698
Aligned: 86
Modelled: 86
Confidence: 99.4%
Identity: 35%
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 1hh2 chain P

3D model

Region: 497 - 689
Aligned: 186
Modelled: 186
Confidence: 99.2%
Identity: 18%
PDB header:transcription regulation
Chain: P: PDB Molecule:n utilization substance protein a;
PDBTitle: crystal structure of nusa from thermotoga maritima

Phyre2

PDB 2z0s chain A domain 2

3D model

Region: 554 - 621
Aligned: 68
Modelled: 68
Confidence: 99.2%
Identity: 25%
Fold: Eukaryotic type KH-domain (KH-domain type I)
Superfamily: Eukaryotic type KH-domain (KH-domain type I)
Family: Eukaryotic type KH-domain (KH-domain type I)

Phyre2
1

c1e3hA_
2

c3cdiA_
3

c3cdjA_
4

c2po2A_
5

c2wnrB_
6

c2nn6B_
7

c2ba1D_
8

c2c37L_
9

c3dd6A_
10

c2wp8B_
11

c1udsA_
12

c2pnzB_
13

c3b4tC_
14

c1r6mA_
15

d1e3ha2
16

c2nn6C_
17

c2wnrC_
18

c3hkmB_
19

c2ba0I_
20

c2nn6E_
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c2cqoA_
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c1q46A_
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c1yz6A_
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c2k4kA_
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c2eqsA_
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c2khjA_
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c1hh2P_
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d2z0sa2
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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1e3hA_



100.0 45 PDB header:polyribonucleotide transferase
Chain: A: PDB Molecule:guanosine pentaphosphate synthetase;
PDBTitle: semet derivative of streptomyces antibioticus pnpase/gpsi2 enzyme
2c3cdiA_



100.0 100 PDB header:transferase
Chain: A: PDB Molecule:polynucleotide phosphorylase;
PDBTitle: crystal structure of e. coli pnpase
3c3cdjA_



100.0 100 PDB header:transferase
Chain: A: PDB Molecule:polynucleotide phosphorylase;
PDBTitle: crystal structure of the e. coli kh/s1 domain truncated2 pnpase
4c2po2A_



100.0 28 PDB header:hydrolase/hydrolase
Chain: A: PDB Molecule:probable exosome complex exonuclease 1;
PDBTitle: crystal structure of the p. abyssi exosome rnase ph ring2 complexed with cdp
5c2wnrB_



100.0 31 PDB header:hydrolase
Chain: B: PDB Molecule:probable exosome complex exonuclease 1;
PDBTitle: the structure of methanothermobacter thermautotrophicus2 exosome core assembly
6c2nn6B_



100.0 22 PDB header:hydrolase/transferase
Chain: B: PDB Molecule:exosome complex exonuclease rrp41;
PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40
7c2ba1D_



100.0 26 PDB header:rna binding protein
Chain: D: PDB Molecule:archaeal exosome complex exonuclease rrp41;
PDBTitle: archaeal exosome core
8c2c37L_



100.0 27 PDB header:hydrolase
Chain: L: PDB Molecule:probable exosome complex exonuclease 1;
PDBTitle: rnase ph core of the archaeal exosome in complex with u82 rna
9c3dd6A_



100.0 25 PDB header:transferase
Chain: A: PDB Molecule:ribonuclease ph;
PDBTitle: crystal structure of rph, an exoribonuclease from bacillus2 anthracis at 1.7 a resolution
10c2wp8B_



100.0 20 PDB header:hydrolase
Chain: B: PDB Molecule:exosome complex component ski6;
PDBTitle: yeast rrp44 nuclease
11c1udsA_



100.0 24 PDB header:transferase
Chain: A: PDB Molecule:ribonuclease ph;
PDBTitle: crystal structure of the trna processing enzyme rnase ph r126a mutant2 from aquifex aeolicus
12c2pnzB_



100.0 20 PDB header:hydrolase/hydrolase
Chain: B: PDB Molecule:probable exosome complex exonuclease 2;
PDBTitle: crystal structure of the p. abyssi exosome rnase ph ring2 complexed with udp and gmp
13c3b4tC_



100.0 24 PDB header:transferase
Chain: C: PDB Molecule:ribonuclease ph;
PDBTitle: crystal structure of mycobacterium tuberculosis rnase ph, the2 mycobacterium tuberculosis structural genomics consortium target3 rv1340
14c1r6mA_



100.0 25 PDB header:transferase
Chain: A: PDB Molecule:ribonuclease ph;
PDBTitle: crystal structure of the trna processing enzyme rnase ph from2 pseudomonas aeruginosa in complex with phosphate
15d1e3ha2



100.0 49 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Ribonuclease PH domain 1-like
16c2nn6C_



100.0 18 PDB header:hydrolase/transferase
Chain: C: PDB Molecule:exosome complex exonuclease rrp43;
PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40
17c2wnrC_



100.0 18 PDB header:hydrolase
Chain: C: PDB Molecule:probable exosome complex exonuclease 2;
PDBTitle: the structure of methanothermobacter thermautotrophicus2 exosome core assembly
18c3hkmB_



100.0 23 PDB header:hydrolase
Chain: B: PDB Molecule:os03g0854200 protein;
PDBTitle: crystal structure of rice(oryza sativa) rrp46
19c2ba0I_



100.0 22 PDB header:rna binding protein
Chain: I: PDB Molecule:archeal exosome rna binding protein rrp42;
PDBTitle: archaeal exosome core
20c2nn6E_



100.0 17 PDB header:hydrolase/transferase
Chain: E: PDB Molecule:exosome complex exonuclease rrp42;
PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40
21c2br2G_



not modelled 100.0 20 PDB header:hydrolase
Chain: G: PDB Molecule:exosome complex exonuclease 2;
PDBTitle: rnase ph core of the archaeal exosome
22c2nn6D_



not modelled 100.0 24 PDB header:hydrolase/transferase
Chain: D: PDB Molecule:exosome complex exonuclease rrp46;
PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40
23c2nn6F_



not modelled 100.0 21 PDB header:hydrolase/transferase
Chain: F: PDB Molecule:exosome component 6;
PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40
24d1e3ha6



not modelled 100.0 51 Fold:Ribonuclease PH domain 2-like
Superfamily:Ribonuclease PH domain 2-like
Family:Ribonuclease PH domain 2-like
25d1e3ha3



not modelled 100.0 51 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Ribonuclease PH domain 1-like
26c2wp8A_



not modelled 100.0 16 PDB header:hydrolase
Chain: A: PDB Molecule:exosome complex component rrp45;
PDBTitle: yeast rrp44 nuclease
27d2je6b1



not modelled 100.0 30 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Ribonuclease PH domain 1-like
28d2ba0d1



not modelled 100.0 29 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Ribonuclease PH domain 1-like
29d2nn6b1



not modelled 100.0 23 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Ribonuclease PH domain 1-like
30d1r6la1



not modelled 100.0 25 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Ribonuclease PH domain 1-like
31d1udsa1



not modelled 100.0 22 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Ribonuclease PH domain 1-like
32d2ba0g1



not modelled 100.0 25 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Ribonuclease PH domain 1-like
33d2je6a1



not modelled 99.9 19 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Ribonuclease PH domain 1-like
34d2nn6e1



not modelled 99.9 20 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Ribonuclease PH domain 1-like
35c3krnB_



not modelled 99.9 18 PDB header:hydrolase
Chain: B: PDB Molecule:protein c14a4.5, confirmed by transcript evidence;
PDBTitle: crystal structure of c. elegans cell-death-related nuclease 5(crn-5)
36d2nn6a1



not modelled 99.9 17 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Ribonuclease PH domain 1-like
37d2nn6c1



not modelled 99.9 17 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Ribonuclease PH domain 1-like
38d1oysa1



not modelled 99.9 30 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Ribonuclease PH domain 1-like
39d2nn6f1



not modelled 99.9 25 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Ribonuclease PH domain 1-like
40d1e3ha5



not modelled 99.9 33 Fold:Ribonuclease PH domain 2-like
Superfamily:Ribonuclease PH domain 2-like
Family:Ribonuclease PH domain 2-like
41d2nn6d1



not modelled 99.9 31 Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Ribonuclease PH domain 1-like
42d1udsa2



not modelled 99.8 19 Fold:Ribonuclease PH domain 2-like
Superfamily:Ribonuclease PH domain 2-like
Family:Ribonuclease PH domain 2-like
43d1r6la2



not modelled 99.7 19 Fold:Ribonuclease PH domain 2-like
Superfamily:Ribonuclease PH domain 2-like
Family:Ribonuclease PH domain 2-like
44d1whua_



not modelled 99.7 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
Family:Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
45d1oysa2



not modelled 99.7 23 Fold:Ribonuclease PH domain 2-like
Superfamily:Ribonuclease PH domain 2-like
Family:Ribonuclease PH domain 2-like
46c2cqoA_



99.6 27 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
47c1q46A_



99.6 24 PDB header:translation
Chain: A: PDB Molecule:translation initiation factor 2 alpha subunit;
PDBTitle: crystal structure of the eif2 alpha subunit from2 saccharomyces cerevisia
48c1yz6A_



99.6 42 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
49d1e3ha1



not modelled 99.5 35 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
Family:Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
50c1q8kA_



not modelled 99.5 29 PDB header:translation
Chain: A: PDB Molecule:eukaryotic translation initiation factor 2
PDBTitle: solution structure of alpha subunit of human eif2
51d2ba0d2



not modelled 99.5 20 Fold:Ribonuclease PH domain 2-like
Superfamily:Ribonuclease PH domain 2-like
Family:Ribonuclease PH domain 2-like
52c2k4kA_



99.5 40 PDB header:rna binding protein
Chain: A: PDB Molecule:general stress protein 13;
PDBTitle: solution structure of gsp13 from bacillus subtilis
53d1q46a2



not modelled 99.5 26 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
54c2eqsA_



99.5 33 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
55d2je6b2



not modelled 99.5 16 Fold:Ribonuclease PH domain 2-like
Superfamily:Ribonuclease PH domain 2-like
Family:Ribonuclease PH domain 2-like
56d2br2b2



not modelled 99.5 15 Fold:Ribonuclease PH domain 2-like
Superfamily:Ribonuclease PH domain 2-like
Family:Ribonuclease PH domain 2-like
57c2khjA_



99.4 35 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
58d2ba0a1



not modelled 99.4 22 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
59d1kl9a2



not modelled 99.4 37 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
60c2oceA_



not modelled 99.4 42 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein pa5201;
PDBTitle: crystal structure of tex family protein pa5201 from2 pseudomonas aeruginosa
61c2khiA_



not modelled 99.4 32 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
62d1go3e1



not modelled 99.4 29 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
63d2nn6b2



not modelled 99.4 15 Fold:Ribonuclease PH domain 2-like
Superfamily:Ribonuclease PH domain 2-like
Family:Ribonuclease PH domain 2-like
64d1sroa_



not modelled 99.4 100 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
65c2ahoB_



not modelled 99.4 30 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
66c2k52A_



not modelled 99.3 30 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
67d2z0sa1



not modelled 99.3 16 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
68c1kl9A_



not modelled 99.3 33 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
69d3bzka4



not modelled 99.3 41 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
70d2nn6h1



not modelled 99.3 20 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
71d2je6i1



not modelled 99.3 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
72c3psiA_



not modelled 99.3 15 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)
73c1hh2P_



99.2 18 PDB header:transcription regulation
Chain: P: PDB Molecule:n utilization substance protein a;
PDBTitle: crystal structure of nusa from thermotoga maritima
74d2z0sa2



99.2 25 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
75d2ahob2



not modelled 99.2 31 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
76d2je6a2



not modelled 99.2 16 Fold:Ribonuclease PH domain 2-like
Superfamily:Ribonuclease PH domain 2-like
Family:Ribonuclease PH domain 2-like
77d2nn6d2



not modelled 99.2 21 Fold:Ribonuclease PH domain 2-like
Superfamily:Ribonuclease PH domain 2-like
Family:Ribonuclease PH domain 2-like
78d1smxa_



not modelled 99.1 31 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
79d1wi5a_



not modelled 99.1 21 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
80c3go5A_



not modelled 99.0 19 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
81c2z0sA_



not modelled 99.0 18 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
82d1y14b1



not modelled 99.0 17 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
83c2ba0A_



not modelled 99.0 23 PDB header:rna binding protein
Chain: A: PDB Molecule:archeal exosome rna binding protein rrp4;
PDBTitle: archaeal exosome core
84c2bh8B_



not modelled 99.0 36 PDB header:transcription
Chain: B: PDB Molecule:1b11;
PDBTitle: combinatorial protein 1b11
85d2ba0a3



not modelled 98.9 31 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
86d2nn6i1



not modelled 98.9 23 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
87d2nn6f2



not modelled 98.9 18 Fold:Ribonuclease PH domain 2-like
Superfamily:Ribonuclease PH domain 2-like
Family:Ribonuclease PH domain 2-like
88c2je6I_



not modelled 98.8 23 PDB header:hydrolase
Chain: I: PDB Molecule:exosome complex rna-binding protein 1;
PDBTitle: structure of a 9-subunit archaeal exosome
89c1go3E_



not modelled 98.7 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
90d1hh2p1



not modelled 98.7 24 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
91c2ba1B_



not modelled 98.7 23 PDB header:rna binding protein
Chain: B: PDB Molecule:archaeal exosome rna binding protein csl4;
PDBTitle: archaeal exosome core
92d2ctka1



not modelled 98.6 20 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
93d1tuaa1



not modelled 98.6 25 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
94c2nn6I_



not modelled 98.6 22 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
95d2ba0g2



not modelled 98.6 14 Fold:Ribonuclease PH domain 2-like
Superfamily:Ribonuclease PH domain 2-like
Family:Ribonuclease PH domain 2-like
96c1l2fA_



not modelled 98.5 18 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
97c2pmzE_



not modelled 98.5 41 PDB header:translation, transferase
Chain: E: PDB Molecule:dna-directed rna polymerase subunit e;
PDBTitle: archaeal rna polymerase from sulfolobus solfataricus
98d2c35b1



not modelled 98.5 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
99c2c35F_



not modelled 98.5 19 PDB header:polymerase
Chain: F: PDB Molecule:dna-directed rna polymerase ii 19 kda
PDBTitle: subunits rpb4 and rpb7 of human rna polymerase ii
100c2e3uA_



not modelled 98.5 22 PDB header:rna binding protein
Chain: A: PDB Molecule:hypothetical protein ph1566;
PDBTitle: crystal structure analysis of dim2p from pyrococcus horikoshii ot3
101d1we8a_



not modelled 98.5 24 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
102c2yqrA_



not modelled 98.4 20 PDB header:rna binding protein
Chain: A: PDB Molecule:kiaa0907 protein;
PDBTitle: solution structure of the kh domain in kiaa0907 protein
103d1j4wa1



not modelled 98.4 23 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
104d1x4ma1



not modelled 98.4 33 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
105c3h0gS_



not modelled 98.4 21 PDB header:transcription
Chain: S: PDB Molecule:dna-directed rna polymerase ii subunit rpb7;
PDBTitle: rna polymerase ii from schizosaccharomyces pombe
106c3n89B_



not modelled 98.4 13 PDB header:cell cycle
Chain: B: PDB Molecule:defective in germ line development protein 3, isoform a;
PDBTitle: kh domains
107c2hh2A_



not modelled 98.4 32 PDB header:rna binding protein
Chain: A: PDB Molecule:kh-type splicing regulatory protein;
PDBTitle: solution structure of the fourth kh domain of ksrp
108c2b8kG_



not modelled 98.4 16 PDB header:transferase
Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kda
PDBTitle: 12-subunit rna polymerase ii
109d1khma_



not modelled 98.4 22 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
110d2ctfa1



not modelled 98.4 17 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
111d1dtja_



not modelled 98.4 24 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
112d1zzka1



not modelled 98.3 22 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
113d1ec6a_



not modelled 98.3 25 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
114c2ckzB_



not modelled 98.3 12 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.
115d1x4na1



not modelled 98.3 23 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
116d1viga_



not modelled 98.3 22 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
117c2dgrA_



not modelled 98.3 17 PDB header:rna binding protein
Chain: A: PDB Molecule:ring finger and kh domain-containing protein 1;
PDBTitle: solution structure of the second kh domain in ring finger2 and kh domain containing protein 1
118d1wvna1



not modelled 98.3 26 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
119d2axya1



not modelled 98.3 19 Fold:Eukaryotic type KH-domain (KH-domain type I)
Superfamily:Eukaryotic type KH-domain (KH-domain type I)
Family:Eukaryotic type KH-domain (KH-domain type I)
120d2nn6a2



not modelled 98.3 13 Fold:Ribonuclease PH domain 2-like
Superfamily:Ribonuclease PH domain 2-like
Family:Ribonuclease PH domain 2-like

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