Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD1897c_(-)_2144458_2144889
DateFri Aug 2 13:30:51 BST 2019
Unique Job ID96c51331362ec5d4
SequenceVRVLVQRVSS ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:47.970 Y:44.053 Z:33.202
Model (left) based on template c2dboA_
Top template information
PDB header:hydrolase
Chain: A: PDB Molecule:d-tyrosyl-trna(tyr) deacylase;
PDBTitle: crystal structure of d-tyr-trna(tyr) deacylase from aquifex aeolicus
Confidence and coverage
Confidence:100.0% Coverage: 98%
140 residues ( 98% 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
1c2dboA_
100.0 45
PDB header:hydrolase
Chain: A: PDB Molecule:d-tyrosyl-trna(tyr) deacylase;
PDBTitle: crystal structure of d-tyr-trna(tyr) deacylase from aquifex aeolicus
2d1jkea_
100.0 44
Fold:DTD-like
Superfamily:DTD-like
Family:DTD-like
3c3ko7E_
100.0 31
PDB header:hydrolase
Chain: E: PDB Molecule:d-tyrosyl-trna(tyr) deacylase;
PDBTitle: dtd from plasmodium falciparum in complex with d-lysine
4d1j7ga_
100.0 45
Fold:DTD-like
Superfamily:DTD-like
Family:DTD-like
5c2okvC_
100.0 40
PDB header:hydrolase
Chain: C: PDB Molecule:probable d-tyrosyl-trna(tyr) deacylase 1;
PDBTitle: c-myc dna unwinding element binding protein
6c5xaqB_
100.0 28
PDB header:hydrolase
Chain: B: PDB Molecule:probable d-tyrosyl-trna(tyr) deacylase 2;
PDBTitle: crystal structure of animalia-specific trna deacylase from mus2 musculus
7d1tc5a_
100.0 24
Fold:DTD-like
Superfamily:DTD-like
Family:DTD-like
8c4rrcA_
61.3 18
PDB header:ligase
Chain: A: PDB Molecule:probable threonine--trna ligase 2;
PDBTitle: n-terminal editing domain of threonyl-trna synthetase from aeropyrum2 pernix with l-thr3aa (snapshot 3)
9c4lnaA_
57.7 21
PDB header:transferase
Chain: A: PDB Molecule:purine nucleoside phosphorylase;
PDBTitle: crystal structure of purine nucleoside phosphorylase i from spirosoma2 linguale dsm 74, nysgrc target 029362
10c2z8nB_
50.2 25
PDB header:lyase
Chain: B: PDB Molecule:27.5 kda virulence protein;
PDBTitle: structural basis for the catalytic mechanism of phosphothreonine lyase
11c2hl2A_
37.2 22
PDB header:ligase
Chain: A: PDB Molecule:threonyl-trna synthetase;
PDBTitle: crystal structure of the editing domain of threonyl-trna2 synthetase from pyrococcus abyssi in complex with an3 analog of seryladenylate
12c4uc0A_
34.9 19
PDB header:transferase
Chain: A: PDB Molecule:purine nucleoside phosphorylase;
PDBTitle: crystal structure of a purine nucleoside phosphorylase (psi-nysgrc-2 029736) from agrobacterium vitis
13c4rrfD_
30.7 16
PDB header:ligase
Chain: D: PDB Molecule:threonine--trna ligase;
PDBTitle: editing domain of threonyl-trna synthetase from methanococcus2 jannaschii with l-ser3aa
14d1s7ia_
29.2 16
Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:DGPF domain (Pfam 04946)
15c5h3iC_
27.7 18
PDB header:lipid binding protein
Chain: C: PDB Molecule:putative acyl-coa-binding protein;
PDBTitle: crystal structure of oryza sativa acyl-coa-binding protein 2
16c3i0uA_
24.6 23
PDB header:lyase
Chain: A: PDB Molecule:phosphothreonine lyase ospf;
PDBTitle: structure of the type iii effector/phosphothreonine lyase ospf from2 shigella flexneri
17d2giab1
22.0 20
Fold:ssDNA-binding transcriptional regulator domain
Superfamily:ssDNA-binding transcriptional regulator domain
Family:Guide RNA binding protein gBP
18c2giaB_
22.0 20
PDB header:translation
Chain: B: PDB Molecule:mitochondrial rna-binding protein 1;
PDBTitle: crystal structures of trypanosoma bruciei mrp1/mrp2
19c5ijmA_
20.2 20
PDB header:lipid binding protein
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of an acyl-coa binding protein (lmjf.17.0620) of2 leishmania major
20d1ofua2
20.2 18
Fold:Bacillus chorismate mutase-like
Superfamily:Tubulin C-terminal domain-like
Family:Tubulin, C-terminal domain
21c4zc0A_
not modelled 19.4 18
PDB header:hydrolase
Chain: A: PDB Molecule:replicative dna helicase;
PDBTitle: structure of a dodecameric bacterial helicase
22c4nsnC_
not modelled 18.8 20
PDB header:transferase
Chain: C: PDB Molecule:purine nucleoside phosphorylase;
PDBTitle: crystal structure of purine nucleoside phosphorylase from2 porphyromonas gingivalis atcc 33277, nysgrc target 030972,3 orthorhombic symmetry
23c3pnrB_
not modelled 18.5 14
PDB header:hydrolase/hydrolase inhibitor
Chain: B: PDB Molecule:pbicp-c;
PDBTitle: structure of pbicp-c in complex with falcipain-2
24d1a9xb2
not modelled 18.2 28
Fold:Flavodoxin-like
Superfamily:Class I glutamine amidotransferase-like
Family:Class I glutamine amidotransferases (GAT)
25c1ofuB_
not modelled 14.7 18
PDB header:bacterial cell division inhibitor
Chain: B: PDB Molecule:cell division protein ftsz;
PDBTitle: crystal structure of sula:ftsz from pseudomonas aeruginosa
26c1k6mA_
not modelled 13.9 6
PDB header:transferase, hydrolase
Chain: A: PDB Molecule:6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2-
PDBTitle: crystal structure of human liver 6-phosphofructo-2-kinase/fructose-2,2 6-bisphosphatase
27c3epyA_
not modelled 13.7 18
PDB header:lipid binding protein
Chain: A: PDB Molecule:acyl-coa-binding domain-containing protein 7;
PDBTitle: crystal structure of human acyl-coa binding domain 7 complexed with2 palmitoyl-coa
28c3bh0A_
not modelled 11.2 11
PDB header:replication
Chain: A: PDB Molecule:dnab-like replicative helicase;
PDBTitle: atpase domain of g40p
29d1rq2a2
not modelled 11.0 19
Fold:Bacillus chorismate mutase-like
Superfamily:Tubulin C-terminal domain-like
Family:Tubulin, C-terminal domain
30d1o51a_
not modelled 10.7 22
Fold:Ferredoxin-like
Superfamily:GlnB-like
Family:DUF190/COG1993
31c4zmiA_
not modelled 10.0 14
PDB header:dna binding protein
Chain: A: PDB Molecule:telomere length regulator taz1;
PDBTitle: crystal structure of the helical domain of s. pombe taz1
32c2wh5A_
not modelled 10.0 18
PDB header:lipid binding protein
Chain: A: PDB Molecule:acyl-coa-binding domain-containing protein 4;
PDBTitle: crystal structure of human acyl-coa binding domain 42 complexed with stearoyl-coa
33c2r6r1_
not modelled 10.0 14
PDB header:cell cycle
Chain: 1: PDB Molecule:cell division protein ftsz;
PDBTitle: aquifex aeolicus ftsz
34c2lbbA_
not modelled 9.7 21
PDB header:protein binding
Chain: A: PDB Molecule:acyl coa binding protein;
PDBTitle: solution structure of acyl coa binding protein from babesia bovis t2bo
35c6bbmA_
not modelled 9.6 17
PDB header:replication
Chain: A: PDB Molecule:replicative dna helicase;
PDBTitle: mechanisms of opening and closing of the bacterial replicative2 helicase: the dnab helicase and lambda p helicase loader complex
36d1s1ma1
not modelled 9.6 21
Fold:Flavodoxin-like
Superfamily:Class I glutamine amidotransferase-like
Family:Class I glutamine amidotransferases (GAT)
37d1tf5a1
not modelled 9.6 33
Fold:Pre-protein crosslinking domain of SecA
Superfamily:Pre-protein crosslinking domain of SecA
Family:Pre-protein crosslinking domain of SecA
38c1st7A_
not modelled 9.5 26
PDB header:transport protein
Chain: A: PDB Molecule:acyl-coa-binding protein;
PDBTitle: solution structure of acyl coenzyme a binding protein from2 yeast
39c2m71A_
not modelled 8.9 10
PDB header:translation
Chain: A: PDB Molecule:translation initiation factor if-3;
PDBTitle: solution structure of the a c-terminal domain of translation2 initiation factor if-3 from campylobacter jejuni
40c5he9E_
not modelled 8.8 17
PDB header:protein binding
Chain: E: PDB Molecule:phage inhibitor protein;
PDBTitle: bacterial initiation protein in complex with phage inhibitor protein
41c5vodD_
not modelled 8.6 60
PDB header:viral protein/immune system
Chain: D: PDB Molecule:envelope glycoprotein ul130;
PDBTitle: crystal structure of hcmv pentamer in complex with neutralizing2 antibody 9i6
42c3tekA_
not modelled 8.5 34
PDB header:dna binding protein
Chain: A: PDB Molecule:thermodbp-single stranded dna binding protein;
PDBTitle: thermodbp: a non-canonical single-stranded dna binding protein with a2 novel structure and mechanism
43c4yheB_
not modelled 8.1 13
PDB header:hydrolase
Chain: B: PDB Molecule:gh5;
PDBTitle: native bacteroidetes-affiliated gh5 cellulase linked with a2 polysaccharide utilization locus
44d1llna_
not modelled 8.0 21
Fold:Ribosome inactivating proteins (RIP)
Superfamily:Ribosome inactivating proteins (RIP)
Family:Plant cytotoxins
45c4m1eC_
not modelled 7.9 22
PDB header:transferase
Chain: C: PDB Molecule:purine nucleoside phosphorylase;
PDBTitle: crystal structure of purine nucleoside phosphorylase i from2 planctomyces limnophilus dsm 3776, nysgrc target 029364.
46c2q6tB_
not modelled 7.7 20
PDB header:hydrolase
Chain: B: PDB Molecule:dnab replication fork helicase;
PDBTitle: crystal structure of the thermus aquaticus dnab monomer
47c4uznA_
not modelled 7.6 36
PDB header:hydrolase
Chain: A: PDB Molecule:endo-beta-1,4-glucanase (celulase b);
PDBTitle: the native structure of the family 46 carbohydrate-binding2 module (cbm46) of endo-beta-1,4-glucanase b (cel5b) from3 bacillus halodurans
48c1bifA_
not modelled 7.6 8
PDB header:bifunctional enzyme
Chain: A: PDB Molecule:6-phosphofructo-2-kinase/ fructose-2,6-bisphosphatase;
PDBTitle: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase bifunctional2 enzyme complexed with atp-g-s and phosphate
49c2copA_
not modelled 7.5 18
PDB header:lipid binding protein
Chain: A: PDB Molecule:acyl-coenzyme a binding domain containing 6;
PDBTitle: solution structure of rsgi ruh-040, an acbp domain from2 human cdna
50d2j44a2
not modelled 7.1 13
Fold:Prealbumin-like
Superfamily:Starch-binding domain-like
Family:PUD-like
51d1a79a1
not modelled 7.0 29
Fold:Restriction endonuclease-like
Superfamily:tRNA-intron endonuclease catalytic domain-like
Family:tRNA-intron endonuclease catalytic domain-like
52d1hb6a_
not modelled 7.0 24
Fold:Acyl-CoA binding protein-like
Superfamily:Acyl-CoA binding protein
Family:Acyl-CoA binding protein
53d1i96v_
not modelled 6.8 12
Fold:IF3-like
Superfamily:Translation initiation factor IF3, C-terminal domain
Family:Translation initiation factor IF3, C-terminal domain
54d1j3ba2
not modelled 6.8 23
Fold:PEP carboxykinase N-terminal domain
Superfamily:PEP carboxykinase N-terminal domain
Family:PEP carboxykinase N-terminal domain
55c3v2uC_
not modelled 6.7 17
PDB header:transcription
Chain: C: PDB Molecule:protein gal3;
PDBTitle: crystal structure of the yeast gal regulon complex of the repressor,2 gal80p, and the transducer, gal3p, with galactose and atp
56c5j67C_
not modelled 6.7 31
PDB header:membrane protein
Chain: C: PDB Molecule:astrotactin-2;
PDBTitle: structure of astrotactin-2, a conserved vertebrate-specific and2 perforin-like membrane protein involved in neuronal development
57c2dclB_
not modelled 6.6 29
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:hypothetical upf0166 protein ph1503;
PDBTitle: structure of ph1503 protein from pyrococcus horikoshii ot3
58c2v4uA_
not modelled 6.5 8
PDB header:ligase
Chain: A: PDB Molecule:ctp synthase 2;
PDBTitle: human ctp synthetase 2 - glutaminase domain in complex with2 5-oxo-l-norleucine
59c2q1yB_
not modelled 6.4 20
PDB header:cell cycle, signaling protein
Chain: B: PDB Molecule:cell division protein ftsz;
PDBTitle: crystal structure of cell division protein ftsz from mycobacterium2 tuberculosis in complex with gtp-gamma-s
60c3h16A_
not modelled 6.4 27
PDB header:signaling protein
Chain: A: PDB Molecule:tir protein;
PDBTitle: crystal structure of a bacteria tir domain, pdtir from paracoccus2 denitrificans
61d1ii2a2
not modelled 6.3 11
Fold:PEP carboxykinase N-terminal domain
Superfamily:PEP carboxykinase N-terminal domain
Family:PEP carboxykinase N-terminal domain
62c3flvA_
not modelled 6.3 18
PDB header:lipid binding protein
Chain: A: PDB Molecule:acyl-coa-binding domain-containing protein 5;
PDBTitle: the crystal structure of human acyl-coenzymea binding domain2 containing 5
63d2ifea_
not modelled 6.3 20
Fold:IF3-like
Superfamily:Translation initiation factor IF3, C-terminal domain
Family:Translation initiation factor IF3, C-terminal domain
64c3fp5A_
not modelled 6.2 18
PDB header:lipid binding protein
Chain: A: PDB Molecule:acyl-coa binding protein;
PDBTitle: crystal structure of acbp from moniliophthora perniciosa
65d1hbka_
not modelled 6.1 18
Fold:Acyl-CoA binding protein-like
Superfamily:Acyl-CoA binding protein
Family:Acyl-CoA binding protein
66c2vawA_
not modelled 6.1 18
PDB header:cell cycle
Chain: A: PDB Molecule:cell division protein ftsz;
PDBTitle: ftsz pseudomonas aeruginosa gdp
67c2pebB_
not modelled 6.1 27
PDB header:oxidoreductase
Chain: B: PDB Molecule:putative dioxygenase;
PDBTitle: crystal structure of a putative dioxygenase (npun_f1925) from nostoc2 punctiforme pcc 73102 at 1.46 a resolution
68c1a79B_
not modelled 5.9 29
PDB header:endonuclease
Chain: B: PDB Molecule:trna endonuclease;
PDBTitle: crystal structure of the trna splicing endonuclease from2 methanococcus jannaschii
69d2ftsa1
not modelled 5.9 21
Fold:beta-clip
Superfamily:MoeA C-terminal domain-like
Family:MoeA C-terminal domain-like
70c5abrB_
not modelled 5.8 20
PDB header:electron transport
Chain: B: PDB Molecule:ferredoxin, 2fe-2s;
PDBTitle: structure of fesi protein from azotobacter vinelandii
71c1keeH_
not modelled 5.8 28
PDB header:ligase
Chain: H: PDB Molecule:carbamoyl-phosphate synthetase small chain;
PDBTitle: inactivation of the amidotransferase activity of carbamoyl phosphate2 synthetase by the antibiotic acivicin
72c3icgD_
not modelled 5.7 18
PDB header:hydrolase
Chain: D: PDB Molecule:endoglucanase d;
PDBTitle: crystal structure of the catalytic and carbohydrate binding domain of2 endoglucanase d from clostridium cellulovorans
73c4zfwA_
not modelled 5.7 21
PDB header:hydrolase
Chain: A: PDB Molecule:rrna n-glycosidase;
PDBTitle: structural studies on a non-toxic homologue of type ii rips from2 momordica charantia (bitter gourd) in complex with galactose.
74c2wjvE_
not modelled 5.5 31
PDB header:hydrolase
Chain: E: PDB Molecule:regulator of nonsense transcripts 2;
PDBTitle: crystal structure of the complex between human nonsense2 mediated decay factors upf1 and upf2
75c4r11F_
not modelled 5.5 29
PDB header:cell adhesion/protein binding
Chain: F: PDB Molecule:cadherin-related hmr-1;
PDBTitle: a conserved phosphorylation switch controls the interaction between2 cadherin and beta-catenin in vitro and in vivo
76c5vbaA_
not modelled 5.5 20
PDB header:chaperone, hydrolase
Chain: A: PDB Molecule:lysozyme, esx-1 secretion-associated protein espg1 chimera;
PDBTitle: structure of espg1 chaperone from the type vii (esx-1) secretion2 system determined with the assistance of n-terminal t4 lysozyme3 fusion
77c1wuuA_
not modelled 5.5 30
PDB header:transferase
Chain: A: PDB Molecule:galactokinase;
PDBTitle: crystal structure of human galactokinase complexed with2 mgamppnp and galactose
78c4e6eA_
not modelled 5.4 21
PDB header:cell cycle
Chain: A: PDB Molecule:cell division protein ftsz;
PDBTitle: crystal structure of a putative cell division protein ftsz (tfu_1113)2 from thermobifida fusca yx-er1 at 2.22 a resolution (psi community3 target, van wezel g.p.)
79c4gfjA_
not modelled 5.4 22
PDB header:isomerase
Chain: A: PDB Molecule:topoisomerase v;
PDBTitle: crystal structure of topo-78, an n-terminal 78kda fragment of2 topoisomerase v
80d1tiga_
not modelled 5.4 19
Fold:IF3-like
Superfamily:Translation initiation factor IF3, C-terminal domain
Family:Translation initiation factor IF3, C-terminal domain
81c2yadA_
not modelled 5.3 20
PDB header:surfactant protein
Chain: A: PDB Molecule:surfactant protein c brichos domain;
PDBTitle: brichos domain of surfactant protein c precursor protein
82c3bgwD_
not modelled 5.3 12
PDB header:replication
Chain: D: PDB Molecule:dnab-like replicative helicase;
PDBTitle: the structure of a dnab-like replicative helicase and its interactions2 with primase

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