Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD2807_(-)_3113668_3114822
DateWed Aug 7 12:50:47 BST 2019
Unique Job IDa917be80650ba451
SequenceVVSTTGMGRS ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:42.703 Y:33.845 Z:48.880
Model (left) based on template c3f9kV_
Top template information
PDB header:viral protein, recombination
Chain: V: PDB Molecule:integrase;
PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd
Confidence and coverage
Confidence:100.0% Coverage: 38%
147 residues ( 38% 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.
235 residues ( 61%) 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
1c3f9kV_
100.0 18
PDB header:viral protein, recombination
Chain: V: PDB Molecule:integrase;
PDBTitle: two domain fragment of hiv-2 integrase in complex with ledgf ibd
2c1c0mA_
100.0 11
PDB header:transferase
Chain: A: PDB Molecule:protein (integrase);
PDBTitle: crystal structure of rsv two-domain integrase
3c3l2tB_
100.0 19
PDB header:recombination/dna
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of the prototype foamy virus (pfv) intasome in2 complex with magnesium and mk0518 (raltegravir)
4c3jcaE_
100.0 13
PDB header:viral protein
Chain: E: PDB Molecule:integrase;
PDBTitle: core model of the mouse mammary tumor virus intasome
5c5m0rF_
100.0 11
PDB header:hydrolase
Chain: F: PDB Molecule:integrase;
PDBTitle: cryo-em reconstruction of the maedi-visna virus (mvv) strand transfer2 complex
6c1ex4A_
100.0 19
PDB header:viral protein
Chain: A: PDB Molecule:integrase;
PDBTitle: hiv-1 integrase catalytic core and c-terminal domain
7d1c0ma2
100.0 11
Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
8c3hpgC_
100.0 12
PDB header:transferase
Chain: C: PDB Molecule:integrase;
PDBTitle: visna virus integrase (residues 1-219) in complex with ledgf2 ibd: examples of open integrase dimer-dimer interfaces
9c5u1cA_
100.0 15
PDB header:viral protein
Chain: A: PDB Molecule:hiv-1 integrase, sso7d chimera;
PDBTitle: structure of tetrameric hiv-1 strand transfer complex intasome
10c3nf9A_
100.0 21
PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:integrase;
PDBTitle: structural basis for a new mechanism of inhibition of hiv integrase2 identified by fragment screening and structure based design
11c5cz1B_
100.0 13
PDB header:hydrolase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of the catalytic core domain of mmtv integrase
12d1asua_
100.0 13
Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
13c4mq3A_
100.0 18
PDB header:viral protein
Chain: A: PDB Molecule:integrase;
PDBTitle: the 1.1 angstrom structure of catalytic core domain of fiv integrase
14c3kksB_
99.9 19
PDB header:dna binding protein
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of catalytic core domain of biv integrase in crystal2 form ii
15d1hyva_
99.9 20
Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
16d1exqa_
99.9 20
Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
17c1k6yB_
99.9 18
PDB header:transferase
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of a two-domain fragment of hiv-1 integrase
18c3dlrA_
99.9 18
PDB header:transferase
Chain: A: PDB Molecule:integrase;
PDBTitle: crystal structure of the catalytic core domain from pfv integrase
19d1cxqa_
99.9 13
Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
20c5ejkG_
99.9 7
PDB header:transferase/dna
Chain: G: PDB Molecule:gag-pro-pol polyprotein;
PDBTitle: crystal structure of the rous sarcoma virus intasome
21d1c6va_
not modelled 99.9 16
Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:Retroviral integrase, catalytic domain
22c5u1cD_
not modelled 99.9 15
PDB header:viral protein
Chain: D: PDB Molecule:hiv-1 integrase, sso7d chimera;
PDBTitle: structure of tetrameric hiv-1 strand transfer complex intasome
23c3l2uA_
not modelled 99.8 14
PDB header:recombination/dna
Chain: A: PDB Molecule:integrase;
PDBTitle: crystal structure of the prototype foamy virus (pfv)2 intasome in complex with magnesium and gs91373 (elvitegravir)
24c4fcyA_
not modelled 99.7 13
PDB header:dna binding protein/dna
Chain: A: PDB Molecule:transposase;
PDBTitle: crystal structure of the bacteriophage mu transpososome
25d1bcoa2
not modelled 99.7 10
Fold:Ribonuclease H-like motif
Superfamily:Ribonuclease H-like
Family:mu transposase, core domain
26c1bcoA_
not modelled 99.6 11
PDB header:transposase
Chain: A: PDB Molecule:bacteriophage mu transposase;
PDBTitle: bacteriophage mu transposase core domain
27c3hosA_
not modelled 99.1 13
PDB header:transferase, dna binding protein/dna
Chain: A: PDB Molecule:transposable element mariner, complete cds;
PDBTitle: crystal structure of the mariner mos1 paired end complex with mg
28c5cr4B_
not modelled 97.4 10
PDB header:hydrolase
Chain: B: PDB Molecule:sleeping beauty transposase, sb100x;
PDBTitle: crystal structure of the sleeping beauty transposase catalytic domain
29c3f2kB_
not modelled 95.6 8
PDB header:transferase
Chain: B: PDB Molecule:histone-lysine n-methyltransferase setmar;
PDBTitle: structure of the transposase domain of human histone-lysine2 n-methyltransferase setmar
30c6paxA_
not modelled 94.2 12
PDB header:gene regulation/dna
Chain: A: PDB Molecule:homeobox protein pax-6;
PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions
31d1pdnc_
not modelled 92.7 14
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
32c1u78A_
not modelled 92.6 14
PDB header:dna binding protein/dna
Chain: A: PDB Molecule:transposable element tc3 transposase;
PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna
33c2f7tA_
not modelled 89.0 9
PDB header:dna binding protein
Chain: A: PDB Molecule:mos1 transposase;
PDBTitle: crystal structure of the catalytic domain of mos1 mariner2 transposase
34c1z4hA_
not modelled 76.8 21
PDB header:protein binding, dna binding protein
Chain: A: PDB Molecule:tor inhibition protein;
PDBTitle: the response regulator tori belongs to a new family of2 atypical excisionase
35c4yo3G_
not modelled 74.2 25
PDB header:transport protein
Chain: G: PDB Molecule:tssa;
PDBTitle: enteroaggregative escherichia coli tssa n-terminal fragment
36c2k27A_
not modelled 72.4 9
PDB header:transcription regulator
Chain: A: PDB Molecule:paired box protein pax-8;
PDBTitle: solution structure of human pax8 paired box domain
37d1zuna1
not modelled 56.8 9
Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Adenine nucleotide alpha hydrolases-like
Family:PAPS reductase-like
38c1zunA_
not modelled 53.4 9
PDB header:transferase
Chain: A: PDB Molecule:sulfate adenylyltransferase subunit 2;
PDBTitle: crystal structure of a gtp-regulated atp sulfurylase2 heterodimer from pseudomonas syringae
39c4j2nB_
not modelled 46.8 16
PDB header:viral protein
Chain: B: PDB Molecule:gp37;
PDBTitle: crystal structure of mycobacteriophage pukovnik xis
40c6dk4A_
not modelled 45.9 15
PDB header:metal transport
Chain: A: PDB Molecule:ferric uptake regulation protein;
PDBTitle: crystal structure of campylobacter jejuni peroxide stress regulator
41c3k32D_
not modelled 43.3 4
PDB header:transferase
Chain: D: PDB Molecule:uncharacterized protein mj0690;
PDBTitle: the crystal structure of predicted subunit of trna methyltransferase2 from methanocaldococcus jannaschii dsm
42c6g7cF_
not modelled 42.8 26
PDB header:transport protein
Chain: F: PDB Molecule:impa-related domain protein;
PDBTitle: nt2-ctd domains of the tssa component from the type vi secretion2 system of aeromonas hydrophila.
43c4j2nA_
not modelled 38.7 18
PDB header:viral protein
Chain: A: PDB Molecule:gp37;
PDBTitle: crystal structure of mycobacteriophage pukovnik xis
44c2yopB_
not modelled 37.3 11
PDB header:apoptosis
Chain: B: PDB Molecule:protein fam3b;
PDBTitle: long wavelength s-sad structure of fam3b pander
45c2kpjA_
not modelled 35.0 17
PDB header:transcription regulator
Chain: A: PDB Molecule:sos-response transcriptional repressor, lexa;
PDBTitle: solution structure of protein sos-response transcriptional2 repressor, lexa from eubacterium rectale. northeast3 structural genomics consortium target err9a
46c6amaO_
not modelled 34.7 24
PDB header:dna binding protein/dna
Chain: O: PDB Molecule:putative dna-binding protein;
PDBTitle: structure of s. coelicolor/s. venezuelae bldc-smea-ssfa complex to2 3.09 angstrom
47c5byhM_
not modelled 34.7 22
PDB header:transferase
Chain: M: PDB Molecule:rna polymerase sigma-54 factor;
PDBTitle: crystal structure of escherichia coli rna polymerase - sigma542 holoenzyme complex
48c3eyyA_
not modelled 32.5 16
PDB header:transport
Chain: A: PDB Molecule:putative iron uptake regulatory protein;
PDBTitle: structural basis for the specialization of nur, a nickel-2 specific fur homologue, in metal sensing and dna3 recognition
49c6fkgC_
not modelled 32.5 15
PDB header:toxin
Chain: C: PDB Molecule:rv1990c (mbca);
PDBTitle: crystal structure of the m.tuberculosis mbct-mbca toxin-antitoxin2 complex.
50c5lc4A_
not modelled 32.1 10
PDB header:signaling protein
Chain: A: PDB Molecule:protein fam3c;
PDBTitle: xray structure of mouse fam3c ilei dimer
51d1ni5a1
not modelled 30.7 7
Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Adenine nucleotide alpha hydrolases-like
Family:PP-loop ATPase
52c3hefB_
not modelled 29.7 37
PDB header:viral protein
Chain: B: PDB Molecule:gene 1 protein;
PDBTitle: crystal structure of the bacteriophage sf6 terminase small subunit
53c1umqA_
not modelled 28.0 26
PDB header:dna-binding protein
Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein;
PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity
54d1umqa_
not modelled 28.0 26
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
55c3ckvA_
not modelled 27.1 12
PDB header:unknown function
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of a mycobacterial protein
56d1adra_
not modelled 23.6 9
Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Phage repressors
57c2xcjB_
not modelled 22.8 22
PDB header:viral protein
Chain: B: PDB Molecule:c protein;
PDBTitle: crystal structure of p2 c, the immunity repressor of2 temperate e. coli phage p2
58c3omtA_
not modelled 21.8 17
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: putative antitoxin component, chu_2935 protein, from xre family from2 prevotella buccae.
59c3h5tA_
not modelled 21.0 15
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from corynebacterium glutamicum
60c5l33A_
not modelled 20.7 22
PDB header:de novo protein
Chain: A: PDB Molecule:denovo ntf2;
PDBTitle: crystal structure of a de novo designed protein with curved beta-sheet
61c2lcvA_
not modelled 20.2 24
PDB header:transcription regulator
Chain: A: PDB Molecule:hth-type transcriptional repressor cytr;
PDBTitle: structure of the cytidine repressor dna-binding domain; an alternate2 calculation
62c2l8nA_
not modelled 19.8 21
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
63c1bdhA_
not modelled 19.6 8
PDB header:transcription/dna
Chain: A: PDB Molecule:protein (purine repressor);
PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex
64c3trbA_
not modelled 19.5 9
PDB header:dna binding protein
Chain: A: PDB Molecule:virulence-associated protein i;
PDBTitle: structure of an addiction module antidote protein of a higa (higa)2 family from coxiella burnetii
65d1efaa1
not modelled 19.3 13
Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
66c5yszA_
not modelled 19.2 33
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: transcriptional regulator celr-cellobiose complex
67c3edpB_
not modelled 18.9 24
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:lin2111 protein;
PDBTitle: the crystal structure of the protein lin2111 (functionally unknown)2 from listeria innocua clip11262
68c3clcC_
not modelled 18.7 4
PDB header:transcription regulator/dna
Chain: C: PDB Molecule:regulatory protein;
PDBTitle: crystal structure of the restriction-modification controller protein2 c.esp1396i tetramer in complex with its natural 35 base-pair operator
69d2bjca1
not modelled 18.3 16
Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
70c1efaA_
not modelled 18.2 15
PDB header:transcription/dna
Chain: A: PDB Molecule:lac repressor;
PDBTitle: crystal structure of the lac repressor dimer bound to operator and the2 anti-inducer onpf
71d1qpza1
not modelled 18.1 4
Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
72c2owlA_
not modelled 18.0 18
PDB header:recombination
Chain: A: PDB Molecule:recombination-associated protein rdgc;
PDBTitle: crystal structure of e. coli rdgc
73c2ebyA_
not modelled 17.6 4
PDB header:transcription
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq;
PDBTitle: crystal structure of a hypothetical protein from e. coli
74d1g2ha_
not modelled 17.2 18
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
75c1g2hA_
not modelled 17.2 18
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein tyrr homolog;
PDBTitle: solution structure of the dna-binding domain of the tyrr2 protein of haemophilus influenzae
76d1utxa_
not modelled 17.2 13
Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
77c6sbsB_
not modelled 16.9 18
PDB header:transcription
Chain: B: PDB Molecule:regulatory protein;
PDBTitle: ytra from sulfolobus acidocaldarius, a gntr-family transcription2 factor
78c4l5eA_
not modelled 16.6 21
PDB header:protein binding
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: crystal structure of a. aeolicus ntrc1 dna binding domain
79c3f8mA_
not modelled 16.5 24
PDB header:transcription
Chain: A: PDB Molecule:gntr-family protein transcriptional regulator;
PDBTitle: crystal structure of phnf from mycobacterium smegmatis
80c3bwgA_
not modelled 16.1 18
PDB header:transcription regulator
Chain: A: PDB Molecule:uncharacterized hth-type transcriptional regulator yydk;
PDBTitle: the crystal structure of possible transcriptional regulator yydk from2 bacillus subtilis subsp. subtilis str. 168
81c6iwqE_
not modelled 16.1 8
PDB header:transferase
Chain: E: PDB Molecule:n-acetylgalactosaminyltransferase 7;
PDBTitle: crystal structure of galnac-t7 with mn2+
82c6gsiI_
not modelled 15.6 18
PDB header:virus
Chain: I: PDB Molecule:vp2;
PDBTitle: feline calicivirus strain f9 bound to a soluble ectodomain fragment of2 feline junctional adhesion molecule a - leading to assembly of a3 portal structure at a unique three-fold axis.
83c6gsiK_
not modelled 15.6 18
PDB header:virus
Chain: K: PDB Molecule:vp2;
PDBTitle: feline calicivirus strain f9 bound to a soluble ectodomain fragment of2 feline junctional adhesion molecule a - leading to assembly of a3 portal structure at a unique three-fold axis.
84d2jn6a1
not modelled 15.4 13
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
85d2icta1
not modelled 15.3 30
Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:SinR domain-like
86d1y9qa1
not modelled 14.9 17
Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:Probable transcriptional regulator VC1968, N-terminal domain
87d1lcda_
not modelled 14.6 16
Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
88c3neuA_
not modelled 14.5 12
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin1836 protein;
PDBTitle: the crystal structure of a functionally-unknown protein lin1836 from2 listeria innocua clip11262
89c2w57A_
not modelled 14.5 14
PDB header:metal transport
Chain: A: PDB Molecule:ferric uptake regulation protein;
PDBTitle: crystal structure of the vibrio cholerae ferric uptake2 regulator (fur) reveals structural rearrangement of the3 dna-binding domains
90c2vpiA_
not modelled 13.9 8
PDB header:ligase
Chain: A: PDB Molecule:gmp synthase;
PDBTitle: human gmp synthetase - glutaminase domain
91c3eetA_
not modelled 13.9 12
PDB header:transcription regulator
Chain: A: PDB Molecule:putative gntr-family transcriptional regulator;
PDBTitle: crystal structure of putative gntr-family transcriptional2 regulator
92d1omza_
not modelled 13.8 11
Fold:Nucleotide-diphospho-sugar transferases
Superfamily:Nucleotide-diphospho-sugar transferases
Family:Exostosin
93d1uxda_
not modelled 13.8 24
Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
94c4i7hA_
not modelled 13.7 14
PDB header:transcription
Chain: A: PDB Molecule:peroxide stress sensing regulator;
PDBTitle: structural basis for peroxide sensing and gene regulation by perr from2 streptococcus pyogenes
95c2m8gX_
not modelled 13.6 11
PDB header:transcription
Chain: X: PDB Molecule:transcriptional regulator;
PDBTitle: structure, function, and tethering of dna-binding domains in 542 transcriptional activators
96c5mm1A_
not modelled 13.5 5
PDB header:membrane protein
Chain: A: PDB Molecule:dolichol monophosphate mannose synthase;
PDBTitle: dolichyl phosphate mannose synthase in complex with gdp and dolichyl2 phosphate mannose
97c3vk0B_
not modelled 13.3 9
PDB header:dna binding protein
Chain: B: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of hypothetical transcription factor nhtf from2 neisseria
98c3cecA_
not modelled 13.2 13
PDB header:transcription
Chain: A: PDB Molecule:putative antidote protein of plasmid maintenance system;
PDBTitle: crystal structure of a putative antidote protein of plasmid2 maintenance system (npun_f2943) from nostoc punctiforme pcc 73102 at3 1.60 a resolution
99c2z86D_
not modelled 13.2 14
PDB header:transferase
Chain: D: PDB Molecule:chondroitin synthase;
PDBTitle: crystal structure of chondroitin polymerase from escherichia coli2 strain k4 (k4cp) complexed with udp-glcua and udp

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