Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD3105c_(prfB)_3472765_3473901
DateThu Aug 8 16:20:28 BST 2019
Unique Job ID586b3d7d966c0514
SequenceMPVTLAAVDP ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:56.921 Y:71.070 Z:59.497
Model (left) based on template d1gqea_
Top template information
Fold:Release factor
Superfamily:Release factor
Family:Release factor
Confidence and coverage
Confidence:100.0% Coverage: 94%
356 residues ( 94% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in JSmol
For other options to view your downloaded structure offline see the FAQ

Sequence analysis 

Download FASTA version

Secondary structure and disorder prediction [Show] 

Domain analysis [Show] 

Detailed template information [Hide] 

 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1gqea_
100.0 42
Fold:Release factor
Superfamily:Release factor
Family:Release factor
2c2ihr1_
100.0 43
PDB header:translation
Chain: 1: PDB Molecule:peptide chain release factor 2;
PDBTitle: rf2 of thermus thermophilus
3c3d5cX_
100.0 36
PDB header:ribosome
Chain: X: PDB Molecule:peptide chain release factor 1;
PDBTitle: structural basis for translation termination on the 70s ribosome. this2 file contains the 30s subunit, release factor 1 (rf1), two trna, and3 mrna molecules of the second 70s ribosome. the entire crystal4 structure contains two 70s ribosomes as described in remark 400.
4d1rq0a_
100.0 35
Fold:Release factor
Superfamily:Release factor
Family:Release factor
5d2b3tb1
100.0 35
Fold:Release factor
Superfamily:Release factor
Family:Release factor
6c1zbtA_
100.0 26
PDB header:translation
Chain: A: PDB Molecule:peptide chain release factor 1;
PDBTitle: crystal structure of peptide chain release factor 1 (rf-1) (smu.1085)2 from streptococcus mutans at 2.34 a resolution
7c2rsmA_
99.9 30
PDB header:translation
Chain: A: PDB Molecule:probable peptide chain release factor c12orf65 homolog,
PDBTitle: solution structure and sirna-mediated knockdown analysis of the2 mitochondrial disease-related protein c12orf65 (ict2)
8c2jy9A_
99.8 27
PDB header:hydrolase
Chain: A: PDB Molecule:putative trna hydrolase domain;
PDBTitle: nmr structure of putative trna hydrolase domain from2 salmonella typhimurium. northeast structural genomics3 consortium target str220
9c2jvaA_
99.7 28
PDB header:hydrolase
Chain: A: PDB Molecule:peptidyl-trna hydrolase domain protein;
PDBTitle: nmr solution structure of peptidyl-trna hydrolase domain protein from2 pseudomonas syringae pv. tomato. northeast structural genomics3 consortium target psr211
10d1j26a_
99.7 26
Fold:dsRBD-like
Superfamily:Peptidyl-tRNA hydrolase domain-like
Family:Peptidyl-tRNA hydrolase domain
11c4v1au_
98.2 18
PDB header:ribosome
Chain: U: PDB Molecule:
PDBTitle: structure of the large subunit of the mammalian mitoribosome, part 22 of 2
12c2lw1A_
96.7 20
PDB header:dna binding protein
Chain: A: PDB Molecule:abc transporter atp-binding protein uup;
PDBTitle: the c-terminal domain of the uup protein is a dna-binding coiled coil2 motif
13c3errB_
89.1 12
PDB header:ligase
Chain: B: PDB Molecule:fusion protein of microtubule binding domain from mouse
PDBTitle: microtubule binding domain from mouse cytoplasmic dynein as a fusion2 with seryl-trna synthetase
14c3layF_
84.1 12
PDB header:metal binding protein
Chain: F: PDB Molecule:zinc resistance-associated protein;
PDBTitle: alpha-helical barrel formed by the decamer of the zinc resistance-2 associated protein (stm4172) from salmonella enterica subsp. enterica3 serovar typhimurium str. lt2
15c1wpaA_
79.4 14
PDB header:cell adhesion
Chain: A: PDB Molecule:occludin;
PDBTitle: 1.5 angstrom crystal structure of human occludin fragment 413-522
16c5n7kD_
73.1 17
PDB header:cell adhesion
Chain: D: PDB Molecule:marvel domain-containing protein 2;
PDBTitle: crystal structure of the coiled-coil domain of human tricellulin
17c2dq0A_
71.7 11
PDB header:ligase
Chain: A: PDB Molecule:seryl-trna synthetase;
PDBTitle: crystal structure of seryl-trna synthetase from pyrococcus2 horikoshii complexed with a seryl-adenylate analog
18c1xawA_
70.2 13
PDB header:cell adhesion
Chain: A: PDB Molecule:occludin;
PDBTitle: crystal structure of the cytoplasmic distal c-terminal2 domain of occludin
19c5yjeA_
69.6 18
PDB header:gene regulation
Chain: A: PDB Molecule:protein hira;
PDBTitle: crystal structure of hira(644-1017)
20d1seta1
61.1 15
Fold:Long alpha-hairpin
Superfamily:tRNA-binding arm
Family:Seryl-tRNA synthetase (SerRS)
21c6h9xA_
not modelled 59.6 13
PDB header:ligase
Chain: A: PDB Molecule:serine--trna ligase;
PDBTitle: klebsiella pneumoniae seryl-trna synthetase in complex with the2 intermediate analog 5'-o-(n-(l-seryl)-sulfamoyl)adenosine
22d2ctka1
not modelled 55.6 16
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)
23c4flaC_
not modelled 55.5 18
PDB header:transcription
Chain: C: PDB Molecule:regulation of nuclear pre-mrna domain-containing protein
PDBTitle: crystal structure of human rprd1b, carboxy-terminal domain
24c6o7ua_
not modelled 50.3 14
PDB header:membrane protein
Chain: A: PDB Molecule:
PDBTitle: saccharomyces cerevisiae v-atpase stv1-vo
25c6gcsY_
not modelled 49.2 13
PDB header:oxidoreductase
Chain: Y: PDB Molecule:nuym subunit;
PDBTitle: cryo-em structure of respiratory complex i from yarrowia lipolytica
26c2jyaA_
not modelled 47.3 13
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein atu1810;
PDBTitle: nmr solution structure of protein atu1810 from agrobacterium2 tumefaciens. northeast structural genomics consortium target atr23,3 ontario centre for structural proteomics target atc1776
27c3lssA_
not modelled 45.0 13
PDB header:ligase
Chain: A: PDB Molecule:seryl-trna synthetase;
PDBTitle: trypanosoma brucei seryl-trna synthetase in complex with atp
28c3qo8A_
not modelled 43.7 5
PDB header:ligase
Chain: A: PDB Molecule:seryl-trna synthetase, cytoplasmic;
PDBTitle: crystal structure of seryl-trna synthetase from candida albicans
29c5lnkc_
not modelled 41.3 27
PDB header:oxidoreductase
Chain: C: PDB Molecule:
PDBTitle: entire ovine respiratory complex i
30d1u5pa2
not modelled 40.7 17
Fold:Spectrin repeat-like
Superfamily:Spectrin repeat
Family:Spectrin repeat
31c1s1hI_
not modelled 38.6 10
PDB header:ribosome
Chain: I: PDB Molecule:40s ribosomal protein s16;
PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from yeast2 obtained by docking atomic models for rna and protein components into3 a 11.7 a cryo-em map. this file, 1s1h, contains 40s subunit. the 60s4 ribosomal subunit is in file 1s1i.
32c2dq3A_
not modelled 36.0 10
PDB header:ligase
Chain: A: PDB Molecule:seryl-trna synthetase;
PDBTitle: crystal structure of aq_298
33c1u5pA_
not modelled 35.1 6
PDB header:structural protein
Chain: A: PDB Molecule:spectrin alpha chain, brain;
PDBTitle: crystal structure of repeats 15 and 16 of chicken brain2 alpha spectrin
34c3pdyB_
not modelled 34.8 12
PDB header:structural protein
Chain: B: PDB Molecule:plectin;
PDBTitle: structure of the third and fourth spectrin repeats of the plakin2 domain of plectin
35d2spca_
not modelled 34.0 9
Fold:Spectrin repeat-like
Superfamily:Spectrin repeat
Family:Spectrin repeat
36c3jbrF_
not modelled 33.3 30
PDB header:membrane protein
Chain: F: PDB Molecule:voltage-dependent calcium channel subunit alpha-2/delta-1;
PDBTitle: cryo-em structure of the rabbit voltage-gated calcium channel cav1.12 complex at 4.2 angstrom
37c3edvB_
not modelled 32.4 14
PDB header:structural protein
Chain: B: PDB Molecule:spectrin beta chain, brain 1;
PDBTitle: crystal structure of repeats 14-16 of beta2-spectrin
38d1cuna2
not modelled 32.4 6
Fold:Spectrin repeat-like
Superfamily:Spectrin repeat
Family:Spectrin repeat
39d1s35a2
not modelled 32.2 8
Fold:Spectrin repeat-like
Superfamily:Spectrin repeat
Family:Spectrin repeat
40d1mqva_
not modelled 32.2 12
Fold:Four-helical up-and-down bundle
Superfamily:Cytochromes
Family:Cytochrome c'-like
41c5o5jI_
not modelled 31.5 26
PDB header:ribosome
Chain: I: PDB Molecule:30s ribosomal protein s9;
PDBTitle: structure of the 30s small ribosomal subunit from mycobacterium2 smegmatis
42c6o7xa_
not modelled 31.2 14
PDB header:membrane protein
Chain: A: PDB Molecule:vacuolar atp synthase catalytic subunit a;
PDBTitle: saccharomyces cerevisiae v-atpase stv1-v1vo state 3
43c5jw9B_
not modelled 29.3 9
PDB header:protein binding
Chain: B: PDB Molecule:rna polymerase ii elongation factor ell2;
PDBTitle: the crystal structure of ell2 oclludin domain and aff4 peptide
44c6g7oA_
not modelled 29.2 14
PDB header:membrane protein
Chain: A: PDB Molecule:alkaline ceramidase 3,soluble cytochrome b562;
PDBTitle: crystal structure of human alkaline ceramidase 3 (acer3) at 2.72 angstrom resolution
45d1u5pa1
not modelled 28.6 6
Fold:Spectrin repeat-like
Superfamily:Spectrin repeat
Family:Spectrin repeat
46c5xauB_
not modelled 28.6 18
PDB header:cell adhesion
Chain: B: PDB Molecule:laminin subunit beta-1;
PDBTitle: crystal structure of integrin binding fragment of laminin-511
47c3pdgA_
not modelled 28.4 12
PDB header:unknown function
Chain: A: PDB Molecule:fibronectin(iii)-like module;
PDBTitle: structures of clostridium thermocellum cbha fibronectin(iii)-like2 modules
48c1f8sA_
not modelled 27.7 23
PDB header:oxidoreductase
Chain: A: PDB Molecule:l-amino acid oxidase;
PDBTitle: crystal structure of l-amino acid oxidase from calloselasma2 rhodostoma, complexed with three molecules of o-aminobenzoate.
49d1gqaa_
not modelled 27.6 14
Fold:Four-helical up-and-down bundle
Superfamily:Cytochromes
Family:Cytochrome c'-like
50c3fpjA_
not modelled 27.4 16
PDB header:biosynthetic protein, transferase
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of e81q mutant of mtnas in complex with s-2 adenosylmethionine
51c5xauC_
not modelled 26.7 19
PDB header:cell adhesion
Chain: C: PDB Molecule:laminin subunit gamma-1;
PDBTitle: crystal structure of integrin binding fragment of laminin-511
52c3s2xB_
not modelled 26.6 27
PDB header:transferase
Chain: B: PDB Molecule:acetyl-coa synthase subunit alpha;
PDBTitle: structure of acetyl-coenzyme a synthase alpha subunit c-terminal2 domain
53d2f66c1
not modelled 26.3 41
Fold:Long alpha-hairpin
Superfamily:Endosomal sorting complex assembly domain
Family:VPS37 C-terminal domain-like
54c3j20K_
not modelled 26.2 21
PDB header:ribosome
Chain: K: PDB Molecule:30s ribosomal protein s9p;
PDBTitle: promiscuous behavior of proteins in archaeal ribosomes revealed by2 cryo-em: implications for evolution of eukaryotic ribosomes (30s3 ribosomal subunit)
55d1nj1a3
not modelled 25.8 14
Fold:Class II aaRS and biotin synthetases
Superfamily:Class II aaRS and biotin synthetases
Family:Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
56d1s35a1
not modelled 25.6 7
Fold:Spectrin repeat-like
Superfamily:Spectrin repeat
Family:Spectrin repeat
57d2vqei1
not modelled 24.6 31
Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Translational machinery components
58c2lvwA_
not modelled 24.4 8
PDB header:transferase
Chain: A: PDB Molecule:acetolactate synthase isozyme 1 small subunit;
PDBTitle: solution nmr studies of the dimeric regulatory subunit ilvn of the2 e.coli acetohydroxyacid synthase i (ahas i)
59c5cx2B_
not modelled 24.2 23
PDB header:structural protein
Chain: B: PDB Molecule:coronin;
PDBTitle: structure of coiled coil domain of leishmania donovani coronin
60c5cx2C_
not modelled 24.2 23
PDB header:structural protein
Chain: C: PDB Molecule:coronin;
PDBTitle: structure of coiled coil domain of leishmania donovani coronin
61c5j4oA_
not modelled 24.1 8
PDB header:structural protein
Chain: A: PDB Molecule:spectrin alpha chain, erythrocytic 1;
PDBTitle: structure of human erythrocytic spectrin alpha chain repeats 16-17
62d2gy9i1
not modelled 23.9 38
Fold:Ribosomal protein S5 domain 2-like
Superfamily:Ribosomal protein S5 domain 2-like
Family:Translational machinery components
63c2z9fC_
not modelled 23.8 29
PDB header:biosynthetic protein
Chain: C: PDB Molecule:cellulose synthase operon protein d;
PDBTitle: crystal structure of axcesd protein from acetobacter xylinum
64c6p2rB_
not modelled 23.5 12
PDB header:transferase
Chain: B: PDB Molecule:dolichyl-phosphate-mannose--protein mannosyltransferase 2;
PDBTitle: structure of s. cerevisiae protein o-mannosyltransferase pmt1-pmt22 complex bound to the sugar donor
65d2pc6a2
not modelled 23.2 13
Fold:Ferredoxin-like
Superfamily:ACT-like
Family:IlvH-like
66d1cpqa_
not modelled 23.2 7
Fold:Four-helical up-and-down bundle
Superfamily:Cytochromes
Family:Cytochrome c'-like
67c2cazF_
not modelled 22.9 38
PDB header:protein transport
Chain: F: PDB Molecule:protein srn2;
PDBTitle: escrt-i core
68d1m0da_
not modelled 22.8 25
Fold:Restriction endonuclease-like
Superfamily:Restriction endonuclease-like
Family:Endonuclease I (Holliday junction resolvase)
69c2e1mA_
not modelled 22.6 22
PDB header:oxidoreductase
Chain: A: PDB Molecule:l-glutamate oxidase;
PDBTitle: crystal structure of l-glutamate oxidase from streptomyces sp. x-119-6
70c6oteA_
not modelled 22.4 11
PDB header:ligase
Chain: A: PDB Molecule:seryl-trna synthetase, cytoplasmic;
PDBTitle: crystal structure of seryl-trna synthetase (serrs) from2 cryptosporidium parvum complexed with l-serylsulfamoyl adenosine
71c3hjtB_
not modelled 21.9 23
PDB header:cell adhesion, transport protein
Chain: B: PDB Molecule:lmb;
PDBTitle: structure of laminin binding protein (lmb) of streptococcus agalactiae2 a bifunctional protein with adhesin and metal transporting activity
72d1ivsa1
not modelled 21.9 15
Fold:Long alpha-hairpin
Superfamily:tRNA-binding arm
Family:Valyl-tRNA synthetase (ValRS) C-terminal domain
73d2fgca2
not modelled 21.7 10
Fold:Ferredoxin-like
Superfamily:ACT-like
Family:IlvH-like
74c3mfqB_
not modelled 21.6 28
PDB header:metal binding protein
Chain: B: PDB Molecule:high-affinity zinc uptake system protein znua;
PDBTitle: a glance into the metal binding specificity of troa: where elaborate2 behaviors occur in the active center
75d1nj8a3
not modelled 21.3 14
Fold:Class II aaRS and biotin synthetases
Superfamily:Class II aaRS and biotin synthetases
Family:Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
76c3bbnI_
not modelled 21.2 25
PDB header:ribosome
Chain: I: PDB Molecule:ribosomal protein s9;
PDBTitle: homology model for the spinach chloroplast 30s subunit fitted to 9.4a2 cryo-em map of the 70s chlororibosome.
77d2axya1
not modelled 21.0 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)
78c5xyiQ_
not modelled 21.0 21
PDB header:ribosome
Chain: Q: PDB Molecule:40s ribosomal protein s16, putative;
PDBTitle: small subunit of trichomonas vaginalis ribosome
79c2r60A_
not modelled 20.6 14
PDB header:transferase
Chain: A: PDB Molecule:glycosyl transferase, group 1;
PDBTitle: structure of apo sucrose phosphate synthase (sps) of2 halothermothrix orenii
80c2xzmI_
not modelled 20.4 15
PDB header:ribosome
Chain: I: PDB Molecule:rps16e;
PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1
81c4r4mB_
not modelled 20.3 27
PDB header:dna binding protein
Chain: B: PDB Molecule:cgmp-dependent protein kinase 1;
PDBTitle: crystal structure of c42l cgmp dependent protein kinase i alpha (pkgi2 alpha) leucine zipper
82c3zeyK_
not modelled 20.2 19
PDB header:ribosome
Chain: K: PDB Molecule:40s ribosomal protein s16, putative;
PDBTitle: high-resolution cryo-electron microscopy structure of the trypanosoma2 brucei ribosome
83c2mi2A_
not modelled 20.2 11
PDB header:transport protein
Chain: A: PDB Molecule:sec-independent protein translocase protein tatb;
PDBTitle: solution structure of the e. coli tatb protein in dpc micelles
84d1pq4a_
not modelled 20.2 26
Fold:Chelatase-like
Superfamily:"Helical backbone" metal receptor
Family:TroA-like
85c3ci9B_
not modelled 20.1 16
PDB header:transcription
Chain: B: PDB Molecule:heat shock factor-binding protein 1;
PDBTitle: crystal structure of the human hsbp1
86d2f1fa1
not modelled 19.9 13
Fold:Ferredoxin-like
Superfamily:ACT-like
Family:IlvH-like
87c2ogwB_
not modelled 19.6 19
PDB header:transport protein
Chain: B: PDB Molecule:high-affinity zinc uptake system protein znua
PDBTitle: structure of abc type zinc transporter from e. coli
88c6p28A_
not modelled 19.4 12
PDB header:transferase
Chain: A: PDB Molecule:dolichyl-phosphate-mannose--protein mannosyltransferase 2;
PDBTitle: crystal structure of the mir domain (aa 337-532) of the s. cerevisiae2 mannosyltransferase pmt2
89c1sryB_
not modelled 19.3 17
PDB header:ligase(synthetase)
Chain: B: PDB Molecule:seryl-trna synthetase;
PDBTitle: refined crystal structure of the seryl-trna synthetase from2 thermus thermophilus at 2.5 angstroms resolution
90d1sd4a_
not modelled 19.3 9
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Penicillinase repressor
91c4cl2A_
not modelled 19.3 16
PDB header:transport protein
Chain: A: PDB Molecule:periplasmic solute binding protein;
PDBTitle: structure of periplasmic metal binding protein from candidatus2 liberibacter asiaticus
92c4ll8E_
not modelled 19.0 10
PDB header:motor protein/transport protein
Chain: E: PDB Molecule:swi5-dependent ho expression protein 3;
PDBTitle: complex of carboxy terminal domain of myo4p and she3p middle fragment
93c3neaA_
not modelled 18.9 36
PDB header:hydrolase
Chain: A: PDB Molecule:peptidyl-trna hydrolase;
PDBTitle: crystal structure of peptidyl-trna hydrolase from francisella2 tularensis
94c2zkqi_
not modelled 18.7 21
PDB header:ribosomal protein/rna
Chain: I: PDB Molecule:
PDBTitle: structure of a mammalian ribosomal 40s subunit within an 80s complex2 obtained by docking homology models of the rna and proteins into an3 8.7 a cryo-em map
95c3kbtA_
not modelled 18.6 13
PDB header:structural protein
Chain: A: PDB Molecule:spectrin beta chain, erythrocyte;
PDBTitle: crystal structure of the ankyrin binding domain of human erythroid2 beta spectrin (repeats 13-15) in complex with the spectrin binding3 domain of human erythroid ankyrin (zu5-ank)
96d2gc9a1
not modelled 18.6 27
Fold:Lipocalins
Superfamily:Lipocalins
Family:Phenolic acid decarboxylase (PAD)
97d2g5ca1
not modelled 18.5 21
Fold:6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like
Family:TyrA dimerization domain-like
98c1qpoA_
not modelled 18.5 19
PDB header:transferase
Chain: A: PDB Molecule:quinolinate acid phosphoribosyl transferase;
PDBTitle: quinolinate phosphoribosyl transferase (qaprtase) apo-enzyme from2 mycobacterium tuberculosis
99c4ak2A_
not modelled 18.2 7
PDB header:heparin-binding protein
Chain: A: PDB Molecule:bt_4661;
PDBTitle: structure of bt4661, a suse-like surface located polysaccharide2 binding protein from the bacteroides thetaiotaomicron heparin3 utilisation locus

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