Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD1701_(xerD)_1926209_1927144
DateFri Aug 2 13:30:30 BST 2019
Unique Job ID9b9d3715e1090991
SequenceMKTLALQLQG ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:89.816 Y:59.949 Z:44.142
Model (left) based on template c5hxyE_
Top template information
PDB header:recombination
Chain: E: PDB Molecule:tyrosine recombinase xera;
PDBTitle: crystal structure of xera recombinase
Confidence and coverage
Confidence:100.0% Coverage: 90%
279 residues ( 90% 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
1c5hxyE_
100.0 27
PDB header:recombination
Chain: E: PDB Molecule:tyrosine recombinase xera;
PDBTitle: crystal structure of xera recombinase
2c5vfzA_
100.0 24
PDB header:dna binding protein
Chain: A: PDB Molecule:gp33;
PDBTitle: integrase from mycobacterium phage brujita
3c5jjvA_
100.0 22
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
4c1a0pA_
100.0 40
PDB header:dna recombination
Chain: A: PDB Molecule:site-specific recombinase xerd;
PDBTitle: site-specific recombinase, xerd
5c1ma7A_
100.0 14
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
6c1crxA_
100.0 14
PDB header:replication/dna
Chain: A: PDB Molecule:cre recombinase;
PDBTitle: cre recombinase/dna complex reaction intermediate i
7c6en2A_
100.0 16
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)
8c2a3vA_
100.0 28
PDB header:recombination
Chain: A: PDB Molecule:site-specific recombinase inti4;
PDBTitle: structural basis for broad dna-specificity in integron recombination
9c1z1bA_
100.0 21
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
10d1p7da_
100.0 20
Fold:DNA breaking-rejoining enzymes
Superfamily:DNA breaking-rejoining enzymes
Family:Lambda integrase-like, catalytic core
11c4a8eA_
100.0 27
PDB header:cell cycle
Chain: A: PDB Molecule:probable tyrosine recombinase xerc-like;
PDBTitle: the structure of a dimeric xer recombinase from archaea
12c5dcfA_
99.9 43
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
13c3nkhB_
99.9 20
PDB header:recombination
Chain: B: PDB Molecule:integrase;
PDBTitle: crystal structure of integrase from mrsa strain staphylococcus aureus
14d1aiha_
99.8 20
Fold:DNA breaking-rejoining enzymes
Superfamily:DNA breaking-rejoining enzymes
Family:Lambda integrase-like, catalytic core
15c5c6kB_
99.8 25
PDB header:hydrolase
Chain: B: PDB Molecule:integrase;
PDBTitle: bacteriophage p2 integrase catalytic domain
16d1a0pa2
99.8 41
Fold:DNA breaking-rejoining enzymes
Superfamily:DNA breaking-rejoining enzymes
Family:Lambda integrase-like, catalytic core
17d1f44a2
99.8 13
Fold:DNA breaking-rejoining enzymes
Superfamily:DNA breaking-rejoining enzymes
Family:Lambda integrase-like, catalytic core
18c3uxuA_
99.7 16
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
19d1ae9a_
99.7 19
Fold:DNA breaking-rejoining enzymes
Superfamily:DNA breaking-rejoining enzymes
Family:Lambda integrase-like, catalytic core
20d5crxb2
99.4 16
Fold:DNA breaking-rejoining enzymes
Superfamily:DNA breaking-rejoining enzymes
Family:Lambda integrase-like, catalytic core
21c3nrwA_
not modelled 99.4 21
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
22d1f44a1
not modelled 99.2 13
Fold:SAM domain-like
Superfamily:lambda integrase-like, N-terminal domain
Family:lambda integrase-like, N-terminal domain
23d1a0pa1
not modelled 99.1 38
Fold:SAM domain-like
Superfamily:lambda integrase-like, N-terminal domain
Family:lambda integrase-like, N-terminal domain
24c2khqA_
not modelled 99.1 15
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
25c2oxoA_
not modelled 99.1 24
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
26c2keyA_
not modelled 99.1 16
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
27c2kd1A_
not modelled 99.0 17
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
28c2kiwA_
not modelled 98.9 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).
29c2kkpA_
not modelled 98.9 19
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).
30c3lysC_
not modelled 98.9 10
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
31c2kj8A_
not modelled 98.9 11
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
32c2kobA_
not modelled 98.9 17
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
33c2kj9A_
not modelled 98.8 13
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
34c2kkvA_
not modelled 98.8 13
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
35c2khvA_
not modelled 98.6 13
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.
36c2kj5A_
not modelled 98.3 16
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
37c2v6eB_
not modelled 96.3 11
PDB header:hydrolase
Chain: B: PDB Molecule:protelemorase;
PDBTitle: protelomerase telk complexed with substrate dna
38c4f43A_
not modelled 93.1 13
PDB header:recombination/dna
Chain: A: PDB Molecule:protelomerase;
PDBTitle: protelomerase tela mutant r255a complexed with caag hairpin dna
39c3sqiA_
not modelled 58.1 19
PDB header:dna binding protein/dna
Chain: A: PDB Molecule:klla0e03807p;
PDBTitle: dna binding domain of ndc10
40c3t79A_
not modelled 58.1 19
PDB header:dna binding protein/dna
Chain: A: PDB Molecule:klla0e03807p;
PDBTitle: ndc10: a platform for inner kinetochore assembly in budding yeast
41d1s7oa_
not modelled 52.6 10
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
42c3mzyA_
not modelled 50.5 11
PDB header:rna binding protein
Chain: A: PDB Molecule:rna polymerase sigma-h factor;
PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a
43c3vdoA_
not modelled 47.2 18
PDB header:dna binding protein/protein binding
Chain: A: PDB Molecule:rna polymerase sigma factor sigk;
PDBTitle: structure of extra-cytoplasmic function(ecf) sigma factor sigk in2 complex with its negative regulator rska from mycobacterium3 tuberculosis
44c5fgmA_
not modelled 22.6 11
PDB header:hydrolase
Chain: A: PDB Molecule:ecf rna polymerase sigma factor sigr;
PDBTitle: streptomyces coelicolor sigr region 4
45c3sohB_
not modelled 20.5 8
PDB header:motor protein
Chain: B: PDB Molecule:flagellar motor switch protein flig;
PDBTitle: architecture of the flagellar rotor
46d1trra_
not modelled 20.3 23
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
47c4cxfA_
not modelled 20.0 13
PDB header:transcription
Chain: A: PDB Molecule:rna polymerase sigma factor cnrh;
PDBTitle: structure of cnrh in complex with the cytosolic domain of cnry
48c6b7qA_
not modelled 15.9 17
PDB header:cell invasion
Chain: A: PDB Molecule:sdea;
PDBTitle: crystal structure of legionella effector protein sdea (lpg2157) aa.2 211-910
49d1vz0a1
not modelled 15.5 19
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
50c3vepA_
not modelled 15.4 7
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
51c3hugA_
not modelled 15.0 18
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
52d2auwa1
not modelled 14.9 20
Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:NE0471 C-terminal domain-like
53d1jhga_
not modelled 13.8 21
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:TrpR-like
Family:Trp repressor, TrpR
54c1r71B_
not modelled 13.2 12
PDB header:transcription/dna
Chain: B: PDB Molecule:transcriptional repressor protein korb;
PDBTitle: crystal structure of the dna binding domain of korb in complex with2 the operator dna
55c2x48B_
not modelled 12.7 28
PDB header:viral protein
Chain: B: PDB Molecule:cag38821;
PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1
56c1umqA_
not modelled 12.1 15
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
57d1umqa_
not modelled 12.1 15
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:FIS-like
58d1v2za_
not modelled 11.8 28
Fold:KaiA/RbsU domain
Superfamily:KaiA/RbsU domain
Family:Circadian clock protein KaiA, C-terminal domain
59d1r8ja1
not modelled 11.8 28
Fold:KaiA/RbsU domain
Superfamily:KaiA/RbsU domain
Family:Circadian clock protein KaiA, C-terminal domain
60c6dvdF_
not modelled 11.7 18
PDB header:transferase/dna
Chain: F: PDB Molecule:ecf rna polymerase sigma factor sigl;
PDBTitle: crystal structure of mycobacterium tuberculosis transcription2 initiation complex(ecf sigma factor l) with 6 nt spacer and bromine3 labelled in position "-11
61c5jwrE_
not modelled 11.5 28
PDB header:transcription regulator
Chain: E: PDB Molecule:circadian clock protein kaia;
PDBTitle: crystal structure of foldswitch-stabilized kaib in complex with the n-2 terminal ci domain of kaic and a dimer of kaia c-terminal domains3 from thermosynechococcus elongatus
62d1sv1a_
not modelled 11.1 28
Fold:KaiA/RbsU domain
Superfamily:KaiA/RbsU domain
Family:Circadian clock protein KaiA, C-terminal domain
63c6in7B_
not modelled 10.6 11
PDB header:transcription
Chain: B: PDB Molecule:rna polymerase sigma-h factor;
PDBTitle: crystal structure of algu in complex with muca(cyto)
64c2e8mA_
not modelled 10.5 16
PDB header:signaling protein
Chain: A: PDB Molecule:epidermal growth factor receptor kinase
PDBTitle: solution structure of the c-terminal sam-domain of2 epidermal growth receptor pathway substrate 8
65c5wurB_
not modelled 10.5 16
PDB header:metal binding protein
Chain: B: PDB Molecule:ecf rna polymerase sigma factor sigw;
PDBTitle: crystal structure of sigw in complex with its anti-sigma rsiw, an2 oxdized form
66d1or7a1
not modelled 10.4 11
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
67d1xsva_
not modelled 10.1 4
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:YlxM/p13-like
68d1fsea_
not modelled 9.9 18
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
69d1hcra_
not modelled 9.8 25
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
70d1ijwc_
not modelled 9.8 25
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Recombinase DNA-binding domain
71c2kq6A_
not modelled 9.3 20
PDB header:transport protein
Chain: A: PDB Molecule:polycystin-2;
PDBTitle: the structure of the ef-hand domain of polycystin-2 suggests a2 mechanism for ca2+-dependent regulation of polycystin-2 channel3 activity
72c2f4qA_
not modelled 9.2 21
PDB header:isomerase
Chain: A: PDB Molecule:type i topoisomerase, putative;
PDBTitle: crystal structure of deinococcus radiodurans topoisomerase ib
73c2mhhA_
not modelled 9.1 20
PDB header:metal binding protein
Chain: A: PDB Molecule:polycystic kidney disease protein 2;
PDBTitle: solution structure of a ef-hand domain from sea urchin polycystin-2
74c2mqkA_
not modelled 8.0 9
PDB header:hydrolase
Chain: A: PDB Molecule:atp-dependent target dna activator b;
PDBTitle: solution structure of n terminal domain of the mub aaa+ atpase
75d1r71a_
not modelled 7.8 12
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:KorB DNA-binding domain-like
Family:KorB DNA-binding domain-like
76c2q1zA_
not modelled 7.6 14
PDB header:transcription
Chain: A: PDB Molecule:rpoe, ecf sige;
PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr
77c3t0yA_
not modelled 7.5 5
PDB header:transcription regulator/protein binding
Chain: A: PDB Molecule:response regulator;
PDBTitle: structure of the phyr anti-anti-sigma domain bound to the anti-sigma2 factor, nepr
78d1ujoa_
not modelled 7.5 17
Fold:CH domain-like
Superfamily:Calponin-homology domain, CH-domain
Family:Calponin-homology domain, CH-domain
79c3frwF_
not modelled 7.5 12
PDB header:structural genomics, unknown function
Chain: F: PDB Molecule:putative trp repressor protein;
PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum
80c2rnjA_
not modelled 6.9 14
PDB header:transcription
Chain: A: PDB Molecule:response regulator protein vrar;
PDBTitle: nmr structure of the s. aureus vrar dna binding domain
81c5of3E_
not modelled 6.8 9
PDB header:replication
Chain: E: PDB Molecule:dna primase large subunit pril;
PDBTitle: crystal structure of the heterotrimeric prislx primase from s.2 solfataricus.
82c2kleA_
not modelled 6.6 24
PDB header:membrane protein
Chain: A: PDB Molecule:polycystin-2;
PDBTitle: isic refined solution structure of the calcium binding2 domain of the c-terminal cytosolic domain of polycystin-2
83c1u78A_
not modelled 6.5 6
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
84c2auvA_
not modelled 6.5 25
PDB header:oxidoreductase
Chain: A: PDB Molecule:potential nad-reducing hydrogenase subunit;
PDBTitle: solution structure of hndac : a thioredoxin-like [2fe-2s]2 ferredoxin involved in the nadp-reducing hydrogenase3 complex
85d1rp3a2
not modelled 6.4 16
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
86c5uxxC_
not modelled 6.4 11
PDB header:dna binding protein/unknown function
Chain: C: PDB Molecule:rna polymerase sigma factor;
PDBTitle: co-crystal structure of the sigma factor rpoe in complex with the2 anti-sigma factor nepr from bartonella quintana
87c5zx3F_
not modelled 6.3 14
PDB header:transcription
Chain: F: PDB Molecule:ecf rna polymerase sigma factor sigh;
PDBTitle: mycobacterium tuberculosis rna polymerase holoenzyme with ecf sigma2 factor sigma h
88c1wwuA_
not modelled 6.1 7
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein flj21935;
PDBTitle: solution structure of the sam_pnt domain of human protein2 flj21935
89c1x3uA_
not modelled 6.0 14
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein fixj;
PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot
90c3i6xC_
not modelled 6.0 10
PDB header:calmodulin-binding, membrane protein
Chain: C: PDB Molecule:ras gtpase-activating-like protein iqgap1;
PDBTitle: crystal structure of the calponin homology domain of iqgap1
91c2lfwA_
not modelled 6.0 6
PDB header:signaling protein
Chain: A: PDB Molecule:phyr sigma-like domain;
PDBTitle: nmr structure of the phyrsl-nepr complex from sphingomonas sp. fr1
92d1smyf2
not modelled 5.9 14
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
93c4r0gA_
not modelled 5.9 22
PDB header:unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of lpg0393 from legionella pneumophila
94c2jpcA_
not modelled 5.9 26
PDB header:dna binding protein
Chain: A: PDB Molecule:ssrb;
PDBTitle: ssrb dna binding protein
95d1a04a1
not modelled 5.8 14
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:C-terminal effector domain of the bipartite response regulators
Family:GerE-like (LuxR/UhpA family of transcriptional regulators)
96d2g7la1
not modelled 5.8 9
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
97d1q08a_
not modelled 5.5 32
Fold:Putative DNA-binding domain
Superfamily:Putative DNA-binding domain
Family:DNA-binding N-terminal domain of transcription activators
98d1h67a_
not modelled 5.5 8
Fold:CH domain-like
Superfamily:Calponin-homology domain, CH-domain
Family:Calponin-homology domain, CH-domain
99c2o8xA_
not modelled 5.5 15
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

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