Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD2646_(-)_2970561_2971559
DateWed Aug 7 12:50:29 BST 2019
Unique Job IDc20083e1e87f4094
SequenceVNTATRVRLA ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:82.916 Y:58.576 Z:54.569
Model (left) based on template c5vfzA_
Top template information
PDB header:dna binding protein
Chain: A: PDB Molecule:gp33;
PDBTitle: integrase from mycobacterium phage brujita
Confidence and coverage
Confidence:100.0% Coverage: 78%
258 residues ( 78% 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.
328 residues ( 99%) 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 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
1c5vfzA_
100.0 24
PDB header:dna binding protein
Chain: A: PDB Molecule:gp33;
PDBTitle: integrase from mycobacterium phage brujita
2c5jjvA_
100.0 23
PDB header:recombination
Chain: A: PDB Molecule:tyrosine recombinase xerh;
PDBTitle: crystal structure of xerh site-specific recombinase bound to2 palindromic difh substrate: post-cleavage complex
3c1z1bA_
100.0 18
PDB header:dna binding protein/dna
Chain: A: PDB Molecule:integrase;
PDBTitle: crystal structure of a lambda integrase dimer bound to a2 coc' core site
4c5hxyE_
100.0 18
PDB header:recombination
Chain: E: PDB Molecule:tyrosine recombinase xera;
PDBTitle: crystal structure of xera recombinase
5d1p7da_
100.0 21
Fold:DNA breaking-rejoining enzymes
Superfamily:DNA breaking-rejoining enzymes
Family:Lambda integrase-like, catalytic core
6c1ma7A_
100.0 15
PDB header:hydrolase, ligase/dna
Chain: A: PDB Molecule:cre recombinase;
PDBTitle: crystal structure of cre site-specific recombinase2 complexed with a mutant dna substrate, loxp-a8/t27
7c1crxA_
100.0 14
PDB header:replication/dna
Chain: A: PDB Molecule:cre recombinase;
PDBTitle: cre recombinase/dna complex reaction intermediate i
8c6en2A_
100.0 21
PDB header:recombination
Chain: A: PDB Molecule:int protein;
PDBTitle: structure of the tn1549 transposon integrase (aa 82-397, r225k) in2 complex with a circular intermediate dna (ci6b-dna)
9c2a3vA_
100.0 20
PDB header:recombination
Chain: A: PDB Molecule:site-specific recombinase inti4;
PDBTitle: structural basis for broad dna-specificity in integron recombination
10c4a8eA_
100.0 22
PDB header:cell cycle
Chain: A: PDB Molecule:probable tyrosine recombinase xerc-like;
PDBTitle: the structure of a dimeric xer recombinase from archaea
11c1a0pA_
100.0 21
PDB header:dna recombination
Chain: A: PDB Molecule:site-specific recombinase xerd;
PDBTitle: site-specific recombinase, xerd
12c5c6kB_
100.0 19
PDB header:hydrolase
Chain: B: PDB Molecule:integrase;
PDBTitle: bacteriophage p2 integrase catalytic domain
13c5dcfA_
100.0 24
PDB header:recombination
Chain: A: PDB Molecule:tyrosine recombinase xerd,dna translocase ftsk;
PDBTitle: c-terminal domain of xerd recombinase in complex with gamma domain of2 ftsk
14d1aiha_
100.0 24
Fold:DNA breaking-rejoining enzymes
Superfamily:DNA breaking-rejoining enzymes
Family:Lambda integrase-like, catalytic core
15c3nkhB_
99.9 16
PDB header:recombination
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of integrase from mrsa strain staphylococcus aureus
16d1a0pa2
99.9 23
Fold:DNA breaking-rejoining enzymes
Superfamily:DNA breaking-rejoining enzymes
Family:Lambda integrase-like, catalytic core
17d1ae9a_
99.9 22
Fold:DNA breaking-rejoining enzymes
Superfamily:DNA breaking-rejoining enzymes
Family:Lambda integrase-like, catalytic core
18d1f44a2
99.9 15
Fold:DNA breaking-rejoining enzymes
Superfamily:DNA breaking-rejoining enzymes
Family:Lambda integrase-like, catalytic core
19c3uxuA_
99.9 13
PDB header:recombination
Chain: A: PDB Molecule:probable integrase;
PDBTitle: the structure of the catalytic domain of the sulfolobus spindle-shaped2 viral integrase reveals an evolutionarily conserved catalytic core3 and supports a mechanism of dna cleavage in trans
20d5crxb2
99.7 17
Fold:DNA breaking-rejoining enzymes
Superfamily:DNA breaking-rejoining enzymes
Family:Lambda integrase-like, catalytic core
21c2khqA_
not modelled 99.6 10
PDB header:dna binding protein
Chain: A: PDB Molecule:integrase;
PDBTitle: solution nmr structure of a phage integrase ssp19472 fragment 59-159 from staphylococcus saprophyticus,3 northeast structural genomics consortium target syr103b
22c2kiwA_
not modelled 99.6 11
PDB header:dna binding protein
Chain: A: PDB Molecule:int protein;
PDBTitle: solution nmr structure of the domain n-terminal to the2 integrase domain of sh1003 from staphylococcus3 haemolyticus. northeast structural genomics consortium4 target shr105f (64-166).
23c2oxoA_
not modelled 99.6 21
PDB header:dna binding protein
Chain: A: PDB Molecule:integrase;
PDBTitle: crystallization and structure determination of the core-2 binding domain of bacteriophage lambda integrase
24c3lysC_
not modelled 99.5 11
PDB header:recombination
Chain: C: PDB Molecule:prophage pi2 protein 01, integrase;
PDBTitle: crystal structure of the n-terminal domain of the prophage pi2 protein2 01 (integrase) from lactococcus lactis, northeast structural genomics3 consortium target kr124f
25c2kobA_
not modelled 99.5 15
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: solution nmr structure of clolep_01837 (fragment 61-160)2 from clostridium leptum. northeast structural genomics3 consortium target qlr8a
26c2kkpA_
not modelled 99.5 14
PDB header:dna binding protein
Chain: A: PDB Molecule:phage integrase;
PDBTitle: solution nmr structure of the phage integrase sam-like2 domain from moth 1796 from moorella thermoacetica.3 northeast structural genomics consortium target mtr39k4 (residues 64-171).
27c2kd1A_
not modelled 99.4 14
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:dna integration/recombination/invertion protein;
PDBTitle: solution nmr structure of the integrase-like domain from2 bacillus cereus ordered locus bc_1272. northeast3 structural genomics consortium target bcr268f
28c3nrwA_
not modelled 99.4 16
PDB header:recombination
Chain: A: PDB Molecule:phage integrase/site-specific recombinase;
PDBTitle: crystal structure of the n-terminal domain of phage integrase/site-2 specific recombinase (tnp) from haloarcula marismortui, northeast3 structural genomics consortium target hmr208a
29c2khvA_
not modelled 99.4 12
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:phage integrase;
PDBTitle: solution nmr structure of protein nmul_a0922 from2 nitrosospira multiformis. northeast structural genomics3 consortium target nmr38b.
30c2kj9A_
not modelled 99.4 12
PDB header:dna binding protein
Chain: A: PDB Molecule:integrase;
PDBTitle: nmr structure of intb phage-integrase-like protein fragment2 90-199 from erwinia carotova subsp. atroseptica: northeast3 structural genomics consortium target ewr217e
31c2keyA_
not modelled 99.4 13
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative phage integrase;
PDBTitle: solution nmr structure of a domain from a putative phage integrase2 protein bf2284 from bacteroides fragilis, northeast structural3 genomics consortium target bfr257c
32c2kj8A_
not modelled 99.4 12
PDB header:dna binding protein
Chain: A: PDB Molecule:putative prophage cps-53 integrase;
PDBTitle: nmr structure of fragment 87-196 from the putative phage2 integrase ints of e. coli: northeast structural genomics3 consortium target er652a, psi-2
33c2kkvA_
not modelled 99.3 7
PDB header:dna binding protein
Chain: A: PDB Molecule:integrase;
PDBTitle: solution nmr structure of an integrase domain from protein spa42882 from salmonella enterica, northeast structural genomics consortium3 target slr105h
34c2kj5A_
not modelled 99.3 15
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:phage integrase;
PDBTitle: solution nmr structure of a domain from a putative phage integrase2 protein nmul_a0064 from nitrosospira multiformis, northeast3 structural genomics consortium target nmr46c
35d1a0pa1
not modelled 99.1 19
Fold:SAM domain-like
Superfamily:lambda integrase-like, N-terminal domain
Family:lambda integrase-like, N-terminal domain
36d1f44a1
not modelled 98.2 15
Fold:SAM domain-like
Superfamily:lambda integrase-like, N-terminal domain
Family:lambda integrase-like, N-terminal domain
37c2v6eB_
not modelled 97.2 21
PDB header:hydrolase
Chain: B: PDB Molecule:protelemorase;
PDBTitle: protelomerase telk complexed with substrate dna
38c4f43A_
not modelled 95.2 17
PDB header:recombination/dna
Chain: A: PDB Molecule:protelomerase;
PDBTitle: protelomerase tela mutant r255a complexed with caag hairpin dna
39c2f4qA_
not modelled 62.9 20
PDB header:isomerase
Chain: A: PDB Molecule:type i topoisomerase, putative;
PDBTitle: crystal structure of deinococcus radiodurans topoisomerase ib
40c2h7fX_
not modelled 48.6 10
PDB header:isomerase/dna
Chain: X: PDB Molecule:dna topoisomerase 1;
PDBTitle: structure of variola topoisomerase covalently bound to dna
41c5fgmA_
not modelled 43.7 22
PDB header:hydrolase
Chain: A: PDB Molecule:ecf rna polymerase sigma factor sigr;
PDBTitle: streptomyces coelicolor sigr region 4
42c3jtzA_
not modelled 14.9 13
PDB header:dna binding protein
Chain: A: PDB Molecule:integrase;
PDBTitle: structure of the arm-type binding domain of hpi integrase
43c2o8xA_
not modelled 13.7 21
PDB header:transcription
Chain: A: PDB Molecule:probable rna polymerase sigma-c factor;
PDBTitle: crystal structure of the "-35 element" promoter recognition domain of2 mycobacterium tuberculosis sigc
44c2nogA_
not modelled 11.1 4
PDB header:dna binding protein
Chain: A: PDB Molecule:iswi protein;
PDBTitle: sant domain structure of xenopus remodeling factor iswi
45d2hh6a1
not modelled 10.3 17
Fold:Left-handed superhelix
Superfamily:BH3980-like
Family:BH3980-like
46c3vepA_
not modelled 9.9 18
PDB header:membrane protein/transcription
Chain: A: PDB Molecule:probable rna polymerase sigma-d factor;
PDBTitle: crystal structure of sigd4 in complex with its negative regulator rsda
47d1zszc1
not modelled 9.3 31
Fold:SspB-like
Superfamily:SspB-like
Family:Stringent starvation protein B, SspB
48d1ou8a_
not modelled 9.0 19
Fold:SspB-like
Superfamily:SspB-like
Family:Stringent starvation protein B, SspB
49c5ow2A_
not modelled 8.4 12
PDB header:viral protein
Chain: A: PDB Molecule:capsid protein;
PDBTitle: japanese encephalitis virus capsid protein
50d1ou9a_
not modelled 8.2 19
Fold:SspB-like
Superfamily:SspB-like
Family:Stringent starvation protein B, SspB
51d1sfka_
not modelled 7.8 4
Fold:Flavivirus capsid protein C
Superfamily:Flavivirus capsid protein C
Family:Flavivirus capsid protein C
52d2aq0a1
not modelled 7.7 13
Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:Hef domain-like
53c6b7qA_
not modelled 7.6 17
PDB header:cell invasion
Chain: A: PDB Molecule:sdea;
PDBTitle: crystal structure of legionella effector protein sdea (lpg2157) aa.2 211-910
54d1yfna1
not modelled 7.3 25
Fold:SspB-like
Superfamily:SspB-like
Family:Stringent starvation protein B, SspB
55d1ofcx1
not modelled 7.0 5
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Myb/SANT domain
56d1dzfa2
not modelled 6.8 20
Fold:RPB5-like RNA polymerase subunit
Superfamily:RPB5-like RNA polymerase subunit
Family:RPB5
57c5of3E_
not modelled 6.7 8
PDB header:replication
Chain: E: PDB Molecule:dna primase large subunit pril;
PDBTitle: crystal structure of the heterotrimeric prislx primase from s.2 solfataricus.
58c2lvsA_
not modelled 6.7 14
PDB header:dna binding protein
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: nmr solution structure of a crispr repeat binding protein
59c3h0gE_
not modelled 6.6 22
PDB header:transcription
Chain: E: PDB Molecule:dna-directed rna polymerases i, ii, and iii subunit rpabc1;
PDBTitle: rna polymerase ii from schizosaccharomyces pombe
60d1khda1
not modelled 6.5 17
Fold:Methionine synthase domain-like
Superfamily:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
Family:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
61c3oouA_
not modelled 6.3 18
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin2118 protein;
PDBTitle: the structure of a protein with unkown function from listeria innocua
62d1hmja_
not modelled 6.2 9
Fold:RPB5-like RNA polymerase subunit
Superfamily:RPB5-like RNA polymerase subunit
Family:RPB5
63d1a41a_
not modelled 5.8 12
Fold:DNA breaking-rejoining enzymes
Superfamily:DNA breaking-rejoining enzymes
Family:Eukaryotic DNA topoisomerase I, catalytic core
64d1r6ra_
not modelled 5.8 4
Fold:Flavivirus capsid protein C
Superfamily:Flavivirus capsid protein C
Family:Flavivirus capsid protein C
65c1r6rA_
not modelled 5.8 4
PDB header:viral protein
Chain: A: PDB Molecule:genome polyprotein;
PDBTitle: solution structure of dengue virus capsid protein reveals a2 new fold
66d1uxca_
not modelled 5.8 17
Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
67d2o3la1
not modelled 5.7 19
Fold:Left-handed superhelix
Superfamily:BH3980-like
Family:BH3980-like
68c4qiwH_
not modelled 5.6 11
PDB header:transcription
Chain: H: PDB Molecule:dna-directed rna polymerase subunit h;
PDBTitle: crystal structure of euryarchaeal rna polymerase from thermococcus2 kodakarensis
69d2auwa1
not modelled 5.6 19
Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:NE0471 C-terminal domain-like
70d1mzga_
not modelled 5.5 21
Fold:SufE/NifU
Superfamily:SufE/NifU
Family:SufE-like
71c2y9zA_
not modelled 5.5 10
PDB header:transcription
Chain: A: PDB Molecule:imitation switch protein 1 (del_atpase);
PDBTitle: chromatin remodeling factor isw1a(del_atpase) in dna complex
72c2l8nA_
not modelled 5.5 13
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional repressor cytr;
PDBTitle: nmr structure of the cytidine repressor dna binding domain in presence2 of operator half-site dna
73c5chhA_
not modelled 5.4 19
PDB header:transcription
Chain: A: PDB Molecule:arac family transcriptional regulator;
PDBTitle: crystal structure of transcriptional regulator cdpr from pseudomonas2 aeruginosa
74c3hugA_
not modelled 5.2 21
PDB header:transcription/membrane protein
Chain: A: PDB Molecule:rna polymerase sigma factor;
PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl
75d1ijwc_
not modelled 5.2 21
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
76d1hcra_
not modelled 5.2 21
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
77d1eika_
not modelled 5.1 13
Fold:RPB5-like RNA polymerase subunit
Superfamily:RPB5-like RNA polymerase subunit
Family:RPB5
78c2kpqA_
not modelled 5.1 17
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: nmr structure of agrobacterium tumefaciens protein atu1219:2 northeast structural genomics consortium target att14

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

Transmembrane helix prediction 

Transmembrane helices have been predicted in your sequence to adopt the topology shown below