Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP77804
DateThu Jan 5 12:32:59 GMT 2012
Unique Job ID932326283466f949

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1j20a2
Top template information
Fold:Argininosuccinate synthetase, C-terminal domain
Superfamily:Argininosuccinate synthetase, C-terminal domain
Family:Argininosuccinate synthetase, C-terminal domain
Confidence and coverage
Confidence: 32.8% Coverage: 6%
31 residues ( 6% of your sequence) have been modelled with 32.8% 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.
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3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MNKSLVAVGVIVALGVVWTGGAWYTGKKIETHLEDMVAQANAQLKLTAPESNLEVSYQNY
Secondary structure 








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

















???

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










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   .........190.........200.........210.........220.........230.........240
Sequence  NADRDGKAISLSGEAQSGRIDAVNEYNQKVQLTFNNLKTDGSSTLASFGERVGNQKLSLE
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??????????









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?




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   .........250.........260.........270.........280.........290.........300
Sequence  KMTISVEGKELALLEGMEISGKSDLVNDGKTINSQLDYSLNSLKVQNQDLGSGKLTLKVG
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??




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??



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?
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   .........310.........320.........330.........340.........350.........360
Sequence  QIDGEAWHQFSQQYNAQTQALLAQPEIANNPELYQEKVTEAFFSALPLMLKGDPVITIAP
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?????????



















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   .........370.........380.........390.........400.........410.........420
Sequence  LSWKNSQGESALNLSLFLKDPATTKEAPQTLAQEVDRSVKSLDAKLTIPVDMATEFMTQV
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?
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   .........430.........440.........450.........460.........470.........480
Sequence  AKLEGYQEDQAKKLAKQQVEGASAMGQMFRLTTLQDNTITTSLQYANGQITLNGQKMSLE
Secondary structure 
















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Disorder 
??????



















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   .........490.........500..
Sequence  DFVGMFAMPALNVPAVPAIPQQ
Secondary structure 












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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 1j20 chain A domain 2

3D model

Region: 456 - 486
Aligned: 31
Modelled: 31
Confidence: 32.8%
Identity: 16%
Fold: Argininosuccinate synthetase, C-terminal domain
Superfamily: Argininosuccinate synthetase, C-terminal domain
Family: Argininosuccinate synthetase, C-terminal domain

Phyre2

PDB 1k92 chain A domain 2

3D model

Region: 461 - 486
Aligned: 26
Modelled: 26
Confidence: 32.4%
Identity: 19%
Fold: Argininosuccinate synthetase, C-terminal domain
Superfamily: Argininosuccinate synthetase, C-terminal domain
Family: Argininosuccinate synthetase, C-terminal domain

Phyre2

PDB 2pfu chain A

3D model

Region: 466 - 497
Aligned: 32
Modelled: 32
Confidence: 29.6%
Identity: 6%
PDB header:transport protein
Chain: A: PDB Molecule:biopolymer transport exbd protein;
PDBTitle: nmr strcuture determination of the periplasmic domain of exbd from2 e.coli

Phyre2

PDB 3oba chain A

3D model

Region: 462 - 477
Aligned: 16
Modelled: 16
Confidence: 25.6%
Identity: 31%
PDB header:hydrolase
Chain: A: PDB Molecule:beta-galactosidase;
PDBTitle: structure of the beta-galactosidase from kluyveromyces lactis

Phyre2

PDB 1bhg chain B

3D model

Region: 462 - 477
Aligned: 16
Modelled: 16
Confidence: 23.4%
Identity: 19%
PDB header:glycosidase
Chain: B: PDB Molecule:beta-glucuronidase;
PDBTitle: human beta-glucuronidase at 2.6 a resolution

Phyre2

PDB 1d6z chain A domain 4

3D model

Region: 448 - 480
Aligned: 33
Modelled: 33
Confidence: 22.6%
Identity: 21%
Fold: N domain of copper amine oxidase-like
Superfamily: Copper amine oxidase, domain N
Family: Copper amine oxidase, domain N

Phyre2

PDB 1nvp chain C

3D model

Region: 462 - 478
Aligned: 17
Modelled: 17
Confidence: 22.5%
Identity: 24%
PDB header:transcription/dna
Chain: C: PDB Molecule:transcription initiation factor iia beta chain;
PDBTitle: human tfiia/tbp/dna complex

Phyre2

PDB 1nvp chain C

3D model

Region: 462 - 478
Aligned: 17
Modelled: 17
Confidence: 22.5%
Identity: 24%
Fold: Transcription factor IIA (TFIIA), beta-barrel domain
Superfamily: Transcription factor IIA (TFIIA), beta-barrel domain
Family: Transcription factor IIA (TFIIA), beta-barrel domain

Phyre2

PDB 3mv1 chain 4

3D model

Region: 462 - 477
Aligned: 16
Modelled: 16
Confidence: 22.5%
Identity: 31%
PDB header:hydrolase
Chain: 4: PDB Molecule:beta-galactosidase;
PDBTitle: e.coli (lacz) beta-galactosidase (r599a) in complex with guanidinium

Phyre2

PDB 3ipf chain A

3D model

Region: 449 - 475
Aligned: 27
Modelled: 27
Confidence: 22.5%
Identity: 15%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of the q251q8_deshy protein from desulfitobacterium2 hafniense. northeast structural genomics consortium target dhr8c.

Phyre2

PDB 3lpg chain A

3D model

Region: 462 - 477
Aligned: 16
Modelled: 16
Confidence: 22.3%
Identity: 19%
PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:beta-glucuronidase;
PDBTitle: structure of e. coli beta-glucuronidase bound with a novel, potent2 inhibitor 3-(2-fluorophenyl)-1-(2-hydroxyethyl)-1-((6-methyl-2-oxo-1,3 2-dihydroquinolin-3-yl)methyl)urea

Phyre2

PDB 2g82 chain A domain 1

3D model

Region: 462 - 479
Aligned: 18
Modelled: 18
Confidence: 22.0%
Identity: 11%
Fold: NAD(P)-binding Rossmann-fold domains
Superfamily: NAD(P)-binding Rossmann-fold domains
Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Phyre2

PDB 1jz6 chain C

3D model

Region: 462 - 477
Aligned: 16
Modelled: 16
Confidence: 21.9%
Identity: 31%
PDB header:hydrolase
Chain: C: PDB Molecule:beta-galactosidase;
PDBTitle: e. coli (lacz) beta-galactosidase in complex with galacto-2 tetrazole

Phyre2

PDB 1nh2 chain C

3D model

Region: 462 - 478
Aligned: 17
Modelled: 17
Confidence: 21.7%
Identity: 18%
PDB header:transcription/dna
Chain: C: PDB Molecule:transcription initiation factor iia large chain;
PDBTitle: crystal structure of a yeast tfiia/tbp/dna complex

Phyre2

PDB 1nh2 chain C

3D model

Region: 462 - 478
Aligned: 17
Modelled: 17
Confidence: 21.7%
Identity: 18%
Fold: Transcription factor IIA (TFIIA), beta-barrel domain
Superfamily: Transcription factor IIA (TFIIA), beta-barrel domain
Family: Transcription factor IIA (TFIIA), beta-barrel domain

Phyre2

PDB 1vc2 chain A domain 1

3D model

Region: 462 - 479
Aligned: 18
Modelled: 18
Confidence: 21.5%
Identity: 11%
Fold: NAD(P)-binding Rossmann-fold domains
Superfamily: NAD(P)-binding Rossmann-fold domains
Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Phyre2

PDB 1yq2 chain C

3D model

Region: 462 - 477
Aligned: 16
Modelled: 16
Confidence: 21.4%
Identity: 19%
PDB header:hydrolase
Chain: C: PDB Molecule:beta-galactosidase;
PDBTitle: beta-galactosidase from arthrobacter sp. c2-2 (isoenzyme c2-2 2-1)

Phyre2

PDB 3bga chain B

3D model

Region: 462 - 477
Aligned: 16
Modelled: 16
Confidence: 20.8%
Identity: 19%
PDB header:hydrolase
Chain: B: PDB Molecule:beta-galactosidase;
PDBTitle: crystal structure of beta-galactosidase from bacteroides2 thetaiotaomicron vpi-5482

Phyre2

PDB 6pax chain A domain 1

3D model

Region: 468 - 480
Aligned: 13
Modelled: 13
Confidence: 20.8%
Identity: 23%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: Paired domain

Phyre2

PDB 2b4r chain O domain 1

3D model

Region: 462 - 479
Aligned: 18
Modelled: 18
Confidence: 18.6%
Identity: 22%
Fold: NAD(P)-binding Rossmann-fold domains
Superfamily: NAD(P)-binding Rossmann-fold domains
Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Phyre2
1

d1j20a2
2

d1k92a2
3

c2pfuA_
4

c3obaA_
5

c1bhgB_
6

d1d6za4
7

c1nvpC_
8

d1nvpc_
9

c3mv14_
10

c3ipfA_
11

c3lpgA_
12

d2g82a1
13

c1jz6C_
14

c1nh2C_
15

d1nh2c_
16

d1vc2a1
17

c1yq2C_
18

c3bgaB_
19

d6paxa1
20

d2b4ro1
21



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Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1j20a2



32.8 16 Fold:Argininosuccinate synthetase, C-terminal domain
Superfamily:Argininosuccinate synthetase, C-terminal domain
Family:Argininosuccinate synthetase, C-terminal domain
2d1k92a2



32.4 19 Fold:Argininosuccinate synthetase, C-terminal domain
Superfamily:Argininosuccinate synthetase, C-terminal domain
Family:Argininosuccinate synthetase, C-terminal domain
3c2pfuA_



29.6 6 PDB header:transport protein
Chain: A: PDB Molecule:biopolymer transport exbd protein;
PDBTitle: nmr strcuture determination of the periplasmic domain of exbd from2 e.coli
4c3obaA_



25.6 31 PDB header:hydrolase
Chain: A: PDB Molecule:beta-galactosidase;
PDBTitle: structure of the beta-galactosidase from kluyveromyces lactis
5c1bhgB_



23.4 19 PDB header:glycosidase
Chain: B: PDB Molecule:beta-glucuronidase;
PDBTitle: human beta-glucuronidase at 2.6 a resolution
6d1d6za4



22.6 21 Fold:N domain of copper amine oxidase-like
Superfamily:Copper amine oxidase, domain N
Family:Copper amine oxidase, domain N
7c1nvpC_



22.5 24 PDB header:transcription/dna
Chain: C: PDB Molecule:transcription initiation factor iia beta chain;
PDBTitle: human tfiia/tbp/dna complex
8d1nvpc_



22.5 24 Fold:Transcription factor IIA (TFIIA), beta-barrel domain
Superfamily:Transcription factor IIA (TFIIA), beta-barrel domain
Family:Transcription factor IIA (TFIIA), beta-barrel domain
9c3mv14_



22.5 31 PDB header:hydrolase
Chain: 4: PDB Molecule:beta-galactosidase;
PDBTitle: e.coli (lacz) beta-galactosidase (r599a) in complex with guanidinium
10c3ipfA_



22.5 15 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of the q251q8_deshy protein from desulfitobacterium2 hafniense. northeast structural genomics consortium target dhr8c.
11c3lpgA_



22.3 19 PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:beta-glucuronidase;
PDBTitle: structure of e. coli beta-glucuronidase bound with a novel, potent2 inhibitor 3-(2-fluorophenyl)-1-(2-hydroxyethyl)-1-((6-methyl-2-oxo-1,3 2-dihydroquinolin-3-yl)methyl)urea
12d2g82a1



22.0 11 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
13c1jz6C_



21.9 31 PDB header:hydrolase
Chain: C: PDB Molecule:beta-galactosidase;
PDBTitle: e. coli (lacz) beta-galactosidase in complex with galacto-2 tetrazole
14c1nh2C_



21.7 18 PDB header:transcription/dna
Chain: C: PDB Molecule:transcription initiation factor iia large chain;
PDBTitle: crystal structure of a yeast tfiia/tbp/dna complex
15d1nh2c_



21.7 18 Fold:Transcription factor IIA (TFIIA), beta-barrel domain
Superfamily:Transcription factor IIA (TFIIA), beta-barrel domain
Family:Transcription factor IIA (TFIIA), beta-barrel domain
16d1vc2a1



21.5 11 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
17c1yq2C_



21.4 19 PDB header:hydrolase
Chain: C: PDB Molecule:beta-galactosidase;
PDBTitle: beta-galactosidase from arthrobacter sp. c2-2 (isoenzyme c2-2 2-1)
18c3bgaB_



20.8 19 PDB header:hydrolase
Chain: B: PDB Molecule:beta-galactosidase;
PDBTitle: crystal structure of beta-galactosidase from bacteroides2 thetaiotaomicron vpi-5482
19d6paxa1



20.8 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
20d2b4ro1



18.6 22 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
21d1yqea1



not modelled 17.2 16 Fold:Phosphorylase/hydrolase-like
Superfamily:AF0625-like
Family:AF0625-like
22d1gado1



not modelled 16.3 22 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
23d1ytfc_



not modelled 16.3 19 Fold:Transcription factor IIA (TFIIA), beta-barrel domain
Superfamily:Transcription factor IIA (TFIIA), beta-barrel domain
Family:Transcription factor IIA (TFIIA), beta-barrel domain
24c1k97A_



not modelled 16.2 19 PDB header:ligase
Chain: A: PDB Molecule:argininosuccinate synthase;
PDBTitle: crystal structure of e. coli argininosuccinate synthetase in complex2 with aspartate and citrulline
25d1zud21



not modelled 15.7 38 Fold:beta-Grasp (ubiquitin-like)
Superfamily:MoaD/ThiS
Family:ThiS
26d1j0xo1



not modelled 14.8 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
27d1obfo1



not modelled 14.5 18 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
28c2gfqC_



not modelled 13.5 19 PDB header:structural genomics, unknown function
Chain: C: PDB Molecule:upf0204 protein ph0006;
PDBTitle: structure of protein of unknown function ph0006 from pyrococcus2 horikoshii
29d1hdgo1



not modelled 13.4 12 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
30d1k78a1



not modelled 13.4 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
31c2w7vB_



not modelled 12.7 17 PDB header:transport protein
Chain: B: PDB Molecule:general secretion pathway protein l;
PDBTitle: periplasmic domain of epsl from vibrio parahaemolyticus
32c3mhaB_



not modelled 12.5 67 PDB header:lipid binding protein
Chain: B: PDB Molecule:lipoprotein lprg;
PDBTitle: crystal structure of lprg from mycobacterium tuberculosis bound to pim
33c2kl0A_



not modelled 11.9 25 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative thiamin biosynthesis this;
PDBTitle: solution nmr structure of rhodopseudomonas palustris rpa3574,2 northeast structural genomics consortium (nesg) target rpr325
34d1x87a_



not modelled 11.5 24 Fold:Urocanase
Superfamily:Urocanase
Family:Urocanase
35c1rm1C_



not modelled 10.9 19 PDB header:transcription/dna
Chain: C: PDB Molecule:transcription initiation factor iia large chain;
PDBTitle: structure of a yeast tfiia/tbp/tata-box dna complex
36c3cmgA_



not modelled 10.8 22 PDB header:hydrolase
Chain: A: PDB Molecule:putative beta-galactosidase;
PDBTitle: crystal structure of putative beta-galactosidase from bacteroides2 fragilis
37d1k8ba_



not modelled 10.6 13 Fold:Ribosome binding domain-like
Superfamily:Translation initiation factor 2 beta, aIF2beta, N-terminal domain
Family:Translation initiation factor 2 beta, aIF2beta, N-terminal domain
38d3cmco1



not modelled 10.5 11 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
39d2caya1



not modelled 10.4 19 Fold:PH domain-like barrel
Superfamily:PH domain-like
Family:VPS36 N-terminal domain-like
40d2odgc1



not modelled 10.4 50 Fold:LEM/SAP HeH motif
Superfamily:LEM domain
Family:LEM domain
41c2jv8A_



not modelled 10.3 24 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein ne1242;
PDBTitle: solution structure of protein ne1242 from nitrosomonas2 europaea. northeast structural genomics consortium target3 net4
42c2gjhA_



not modelled 10.3 20 PDB header:de novo protein
Chain: A: PDB Molecule:designed protein;
PDBTitle: nmr structure of cfr (c-terminal fragment of2 computationally designed novel-topology protein top7)
43c1ifpA_



not modelled 10.2 29 PDB header:virus
Chain: A: PDB Molecule:major coat protein assembly;
PDBTitle: inovirus (filamentous bacteriophage) strain pf3 major coat2 protein assembly
44d1dm9a_



not modelled 10.2 31 Fold:Alpha-L RNA-binding motif
Superfamily:Alpha-L RNA-binding motif
Family:Heat shock protein 15 kD
45c1dm9A_



not modelled 10.2 31 PDB header:structural genomics
Chain: A: PDB Molecule:hypothetical 15.5 kd protein in mrca-pcka
PDBTitle: heat shock protein 15 kd
46d3gpdg1



not modelled 10.0 12 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
47c1kskA_



not modelled 9.5 15 PDB header:lyase
Chain: A: PDB Molecule:ribosomal small subunit pseudouridine synthase a;
PDBTitle: structure of rsua
48d1dssg1



not modelled 9.4 17 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
49c1tygG_



not modelled 9.3 25 PDB header:biosynthetic protein
Chain: G: PDB Molecule:yjbs;
PDBTitle: structure of the thiazole synthase/this complex
50d2cu3a1



not modelled 9.3 45 Fold:beta-Grasp (ubiquitin-like)
Superfamily:MoaD/ThiS
Family:ThiS
51c2cqjA_



not modelled 9.2 8 PDB header:rna binding protein
Chain: A: PDB Molecule:u3 small nucleolar ribonucleoprotein protein
PDBTitle: solution structure of the s4 domain of u3 small nucleolar2 ribonucleoprotein protein imp3 homolog
52d1dk7a_



not modelled 9.0 11 Fold:The "swivelling" beta/beta/alpha domain
Superfamily:GroEL apical domain-like
Family:GroEL-like chaperone, apical domain
53c1kh2D_



not modelled 9.0 15 PDB header:ligase
Chain: D: PDB Molecule:argininosuccinate synthetase;
PDBTitle: crystal structure of thermus thermophilus hb82 argininosuccinate synthetase in complex with atp
54c3iz6I_



not modelled 8.9 36 PDB header:ribosome
Chain: I: PDB Molecule:40s ribosomal protein s16 (s9p);
PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome
55d1oela2



not modelled 8.7 11 Fold:The "swivelling" beta/beta/alpha domain
Superfamily:GroEL apical domain-like
Family:GroEL-like chaperone, apical domain
56c3c8vA_



not modelled 8.7 23 PDB header:transferase
Chain: A: PDB Molecule:putative acetyltransferase;
PDBTitle: crystal structure of putative acetyltransferase (yp_390128.1) from2 desulfovibrio desulfuricans g20 at 2.28 a resolution
57d1vioa2



not modelled 8.6 8 Fold:Alpha-L RNA-binding motif
Superfamily:Alpha-L RNA-binding motif
Family:Pseudouridine synthase RsuA N-terminal domain
58d1srva_



not modelled 8.6 25 Fold:The "swivelling" beta/beta/alpha domain
Superfamily:GroEL apical domain-like
Family:GroEL-like chaperone, apical domain
59d1u8fo1



not modelled 8.5 24 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
60c1spfA_



not modelled 8.4 46 PDB header:lipoprotein(surface film)
Chain: A: PDB Molecule:pulmonary surfactant-associated polypeptide c;
PDBTitle: the nmr structure of the pulmonary surfactant-associated2 polypeptide sp-c in an apolar solvent contains a valyl-3 rich alpha-helix
61c1zeqX_



not modelled 8.4 8 PDB header:metal binding protein
Chain: X: PDB Molecule:cation efflux system protein cusf;
PDBTitle: 1.5 a structure of apo-cusf residues 6-88 from escherichia2 coli
62d1tygb_



not modelled 8.3 25 Fold:beta-Grasp (ubiquitin-like)
Superfamily:MoaD/ThiS
Family:ThiS
63c2zkqi_



not modelled 8.2 45 PDB header:ribosomal protein/rna
Chain: I: PDB Molecule:
PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map
64d2pila_



not modelled 8.1 11 Fold:Pili subunits
Superfamily:Pili subunits
Family:Pilin
65d1kh0a_



not modelled 7.9 26 Fold:beta-Grasp (ubiquitin-like)
Superfamily:Immunoglobulin-binding domains
Family:Immunoglobulin-binding domains
66c3m6cA_



not modelled 7.8 22 PDB header:chaperone
Chain: A: PDB Molecule:60 kda chaperonin 1;
PDBTitle: crystal structure of mycobacterium tuberculosis groel1 apical domain
67c2kd2A_



not modelled 7.8 26 PDB header:apoptosis
Chain: A: PDB Molecule:fas apoptotic inhibitory molecule 1;
PDBTitle: nmr structure of faim-ctd
68c3fn9B_



not modelled 7.8 33 PDB header:hydrolase
Chain: B: PDB Molecule:putative beta-galactosidase;
PDBTitle: crystal structure of putative beta-galactosidase from bacteroides2 fragilis
69d1gwma_



not modelled 7.7 7 Fold:Galactose-binding domain-like
Superfamily:Galactose-binding domain-like
Family:Family 29 carbohydrate binding module, CBM29
70d1v6ga2



not modelled 7.6 27 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:LIM domain
71d1sjpa2



not modelled 7.5 25 Fold:The "swivelling" beta/beta/alpha domain
Superfamily:GroEL apical domain-like
Family:GroEL-like chaperone, apical domain
72c3dh3C_



not modelled 7.5 29 PDB header:isomerase/rna
Chain: C: PDB Molecule:ribosomal large subunit pseudouridine synthase f;
PDBTitle: crystal structure of rluf in complex with a 22 nucleotide2 rna substrate
73c2jwlB_



not modelled 7.3 10 PDB header:membrane protein
Chain: B: PDB Molecule:protein tolr;
PDBTitle: solution structure of periplasmic domain of tolr from h.2 influenzae with saxs data
74c3pcqX_



not modelled 7.1 24 PDB header:photosynthesis
Chain: X: PDB Molecule:photosystem i 4.8k protein;
PDBTitle: femtosecond x-ray protein nanocrystallography
75d1b77a2



not modelled 7.1 19 Fold:DNA clamp
Superfamily:DNA clamp
Family:DNA polymerase processivity factor
76d1z45a1



not modelled 7.1 18 Fold:Supersandwich
Superfamily:Galactose mutarotase-like
Family:Aldose 1-epimerase (mutarotase)
77c3mk7B_



not modelled 7.1 20 PDB header:oxidoreductase
Chain: B: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit o;
PDBTitle: the structure of cbb3 cytochrome oxidase
78c3em0A_



not modelled 7.1 14 PDB header:lipid binding protein
Chain: A: PDB Molecule:ileal bile acid-binding protein;
PDBTitle: crystal structure of zebrafish ileal bile acid-bindin protein2 complexed with cholic acid (crystal form b).
79c3e8tA_



not modelled 7.0 11 PDB header:transport protein
Chain: A: PDB Molecule:takeout-like protein 1;
PDBTitle: crystal structure of epiphyas postvittana takeout 1
80c1s1hI_



not modelled 7.0 36 PDB header:ribosome
Chain: I: PDB Molecule:40s ribosomal protein s16;
PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i.
81d1we3a2



not modelled 7.0 25 Fold:The "swivelling" beta/beta/alpha domain
Superfamily:GroEL apical domain-like
Family:GroEL-like chaperone, apical domain
82d1sjpa3



not modelled 6.9 13 Fold:GroEL-intermediate domain like
Superfamily:GroEL-intermediate domain like
Family:GroEL-like chaperone, intermediate domain
83d1ffva2



not modelled 6.9 22 Fold:beta-Grasp (ubiquitin-like)
Superfamily:2Fe-2S ferredoxin-like
Family:2Fe-2S ferredoxin domains from multidomain proteins
84c1vioA_



not modelled 6.9 15 PDB header:lyase
Chain: A: PDB Molecule:ribosomal small subunit pseudouridine synthase a;
PDBTitle: crystal structure of pseudouridylate synthase
85d2axtj1



not modelled 6.8 26 Fold:Single transmembrane helix
Superfamily:Photosystem II reaction center protein J, PsbJ
Family:PsbJ-like
86d1pdnc_



not modelled 6.6 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
87c2wj7D_



not modelled 6.6 47 PDB header:chaperone
Chain: D: PDB Molecule:alpha-crystallin b chain;
PDBTitle: human alphab crystallin
88c2ci8A_



not modelled 6.6 26 PDB header:translation
Chain: A: PDB Molecule:cytoplasmic protein nck1;
PDBTitle: sh2 domain of human nck1 adaptor protein - uncomplexed
89d1kida_



not modelled 6.5 38 Fold:The "swivelling" beta/beta/alpha domain
Superfamily:GroEL apical domain-like
Family:GroEL-like chaperone, apical domain
90d2p4pa1



not modelled 6.5 17 Fold:FAD-binding/transporter-associated domain-like
Superfamily:FAD-binding/transporter-associated domain-like
Family:CorC/HlyC domain-like
91d2pkqo1



not modelled 6.5 13 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
92c3r45C_



not modelled 6.5 18 PDB header:nuclear protein
Chain: C: PDB Molecule:holliday junction recognition protein;
PDBTitle: structure of a cenp-a-histone h4 heterodimer in complex with chaperone2 hjurp
93d1yqga1



not modelled 6.5 18 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like
Family:ProC C-terminal domain-like
94d1of5b_



not modelled 6.4 24 Fold:Cystatin-like
Superfamily:NTF2-like
Family:NTF2-like
95d1rm6c2



not modelled 6.3 44 Fold:beta-Grasp (ubiquitin-like)
Superfamily:2Fe-2S ferredoxin-like
Family:2Fe-2S ferredoxin domains from multidomain proteins
96d2ahra1



not modelled 6.3 13 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like
Family:ProC C-terminal domain-like
97d1czda2



not modelled 6.3 16 Fold:DNA clamp
Superfamily:DNA clamp
Family:DNA polymerase processivity factor
98c3a1zC_



not modelled 6.3 10 PDB header:transport protein
Chain: C: PDB Molecule:hemolymph juvenile hormone binding protein;
PDBTitle: crystal structure of juvenile hormone binding protein from silkworm
99d1dgja2



not modelled 6.3 25 Fold:beta-Grasp (ubiquitin-like)
Superfamily:2Fe-2S ferredoxin-like
Family:2Fe-2S ferredoxin domains from multidomain proteins

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