Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD2104c_(-)_2364535_2364789
DateMon Aug 5 13:25:22 BST 2019
Unique Job IDdcff93639e4bbe10
SequenceMRTTVTLDDD ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:28.347 Y:40.663 Z:31.192
Model (left) based on template c5x3tA_
Top template information
PDB header:antitoxin/toxin
Chain: A: PDB Molecule:antitoxin vapb26;
PDBTitle: vapbc from mycobacterium tuberculosis
Confidence and coverage
Confidence: 95.0% Coverage: 54%
45 residues ( 54% of your sequence) have been modelled with 95.0% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
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
1c5x3tA_
95.0 31
PDB header:antitoxin/toxin
Chain: A: PDB Molecule:antitoxin vapb26;
PDBTitle: vapbc from mycobacterium tuberculosis
2c2bj3D_
92.3 19
PDB header:transcription
Chain: D: PDB Molecule:nickel responsive regulator;
PDBTitle: nikr-apo
3c1q5vB_
89.8 31
PDB header:transcription
Chain: B: PDB Molecule:nickel responsive regulator;
PDBTitle: apo-nikr
4d2bj7a1
88.5 19
Fold:Ribbon-helix-helix
Superfamily:Ribbon-helix-helix
Family:CopG-like
5c2ca9B_
87.5 22
PDB header:transcription
Chain: B: PDB Molecule:putative nickel-responsive regulator;
PDBTitle: apo-nikr from helicobacter pylori in closed trans-2 conformation
6d2hzaa1
86.6 30
Fold:Ribbon-helix-helix
Superfamily:Ribbon-helix-helix
Family:CopG-like
7d2hzab1
85.5 30
Fold:Ribbon-helix-helix
Superfamily:Ribbon-helix-helix
Family:CopG-like
8d2bsqe1
76.4 15
Fold:Ribbon-helix-helix
Superfamily:Ribbon-helix-helix
Family:Trafficking protein A-like
9d1p94a_
76.3 18
Fold:Ribbon-helix-helix
Superfamily:Ribbon-helix-helix
Family:CopG-like
10c2h1oH_
71.9 15
PDB header:gene regulation/dna complex
Chain: H: PDB Molecule:trafficking protein a;
PDBTitle: structure of fitab bound to ir36 dna fragment
11c6noyB_
70.4 22
PDB header:structural protein
Chain: B: PDB Molecule:maintenance of carboxysome positioning b protein, mcsb;
PDBTitle: structure of cyanothece mcdb
12c2k5jB_
69.8 17
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein yiif;
PDBTitle: solution structure of protein yiif from shigella flexneri2 serotype 5b (strain 8401) . northeast structural genomics3 consortium target sft1
13c5yrzC_
54.8 29
PDB header:antitoxin/hydrolase
Chain: C: PDB Molecule:hicb;
PDBTitle: toxin-antitoxin complex from streptococcus pneumoniae
14c6a7vU_
53.4 28
PDB header:toxin/antitoxin
Chain: U: PDB Molecule:antitoxin vapb11;
PDBTitle: crystal structure of mycobacterium tuberculosis vapbc11 toxin-2 antitoxin complex
15c6g1nB_
53.3 18
PDB header:antitoxin
Chain: B: PDB Molecule:antitoxin hicb;
PDBTitle: crystal structure of the burkholderia pseudomallei antitoxin hicb
16c3kk4B_
46.3 13
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein bp1543;
PDBTitle: uncharacterized protein bp1543 from bordetella pertussis tohama i
17c2k29A_
41.6 16
PDB header:transcription
Chain: A: PDB Molecule:antitoxin relb;
PDBTitle: structure of the dbd domain of e. coli antitoxin relb
18c4p7dA_
38.7 9
PDB header:toxin
Chain: A: PDB Molecule:antitoxin hicb3;
PDBTitle: antitoxin hicb3 crystal structure
19d2cpga_
33.2 24
Fold:Ribbon-helix-helix
Superfamily:Ribbon-helix-helix
Family:CopG-like
20c1ea4K_
33.2 24
PDB header:gene regulation/dna
Chain: K: PDB Molecule:transcriptional repressor copg;
PDBTitle: transcriptional repressor copg/22bp dsdna complex
21c6iyaD_
not modelled 30.2 28
PDB header:antitoxin
Chain: D: PDB Molecule:transcriptional regulator copg family;
PDBTitle: structure of the dna binding domain of antitoxin copaso
22c4wyhA_
not modelled 25.2 21
PDB header:replication
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of prix from the hyperthermophilic archaeon2 sulfolobus solfataricus
23d2b4jc1
not modelled 22.4 16
Fold:N-cbl like
Superfamily:HIV integrase-binding domain
Family:HIV integrase-binding domain
24c1z9eA_
not modelled 22.2 16
PDB header:protein binding/transcription
Chain: A: PDB Molecule:pc4 and sfrs1 interacting protein 2;
PDBTitle: solution structure of the hiv-1 integrase-binding domain in2 ledgf/p75
25c6bwqB_
not modelled 22.1 9
PDB header:metal binding protein
Chain: B: PDB Molecule:pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel
PDBTitle: larc2, the c-terminal domain of a cyclometallase involved in the2 synthesis of the npn cofactor of lactate racemase, in complex with3 mnctp
26c4pg8B_
not modelled 21.1 42
PDB header:oxidoreductase
Chain: B: PDB Molecule:homoserine dehydrogenase;
PDBTitle: crystal structure of s. aureus homoserine dehydrogenase at ph8.5
27c5ux1D_
not modelled 19.9 20
PDB header:lyase
Chain: D: PDB Molecule:trna-(ms(2)io(6)a)-hydroxylase-like;
PDBTitle: protein 43 with aldehyde deformylating oxygenase activity from2 synechococcus
28d1vhib_
not modelled 19.6 38
Fold:Ferredoxin-like
Superfamily:Viral DNA-binding domain
Family:Viral DNA-binding domain
29c6qeqD_
not modelled 18.3 18
PDB header:dna binding protein
Chain: D: PDB Molecule:pcff;
PDBTitle: pcff from enterococcus faecalis pcf10
30c2mtnA_
not modelled 18.0 16
PDB header:transferase/protein binding
Chain: A: PDB Molecule:histone-lysine n-methyltransferase 2a, pc4 and sfrs1-
PDBTitle: solution structure of mll-ibd complex
31d1b3ta_
not modelled 16.7 38
Fold:Ferredoxin-like
Superfamily:Viral DNA-binding domain
Family:Viral DNA-binding domain
32c6emoA_
not modelled 16.6 16
PDB header:transcription
Chain: A: PDB Molecule:pc4 and sfrs1-interacting protein,ledgf/p75 ibd-jpo2 m1;
PDBTitle: solution structure of the ledgf/p75 ibd - jpo2 (aa 1-32) complex
33c6emqA_
not modelled 16.4 16
PDB header:transcription
Chain: A: PDB Molecule:pc4 and sfrs1-interacting protein,histone-lysine n-
PDBTitle: solution structure of the ledgf/p75 ibd - mll1 (aa 111-160) complex
34c2mdvB_
not modelled 13.9 16
PDB header:de novo protein
Chain: B: PDB Molecule:designed protein;
PDBTitle: nmr structure of beta alpha alpha 38
35c3kxeD_
not modelled 13.7 21
PDB header:protein binding
Chain: D: PDB Molecule:antitoxin protein pard-1;
PDBTitle: a conserved mode of protein recognition and binding in a2 pard-pare toxin-antitoxin complex
36c3qf7D_
not modelled 13.0 33
PDB header:hydrolase
Chain: D: PDB Molecule:mre11;
PDBTitle: the mre11:rad50 complex forms an atp dependent molecular clamp in dna2 double-strand break repair
37c3do5A_
not modelled 12.9 24
PDB header:oxidoreductase
Chain: A: PDB Molecule:homoserine dehydrogenase;
PDBTitle: crystal structure of putative homoserine dehydrogenase (np_069768.1)2 from archaeoglobus fulgidus at 2.20 a resolution
38c3fxeA_
not modelled 12.7 80
PDB header:unknown function
Chain: A: PDB Molecule:protein icmq;
PDBTitle: crystal structure of interacting domains of icmr and icmq (seleno-2 derivative)
39c4kmaA_
not modelled 12.7 27
PDB header:protein binding
Chain: A: PDB Molecule:gm14141p;
PDBTitle: crystal structure of drosophila suppressor of fused
40c4fxeB_
not modelled 12.5 16
PDB header:toxin/toxin inhibitor
Chain: B: PDB Molecule:antitoxin relb;
PDBTitle: crystal structure of the intact e. coli relbe toxin-antitoxin complex
41c3ai9X_
not modelled 12.3 17
PDB header:transferase
Chain: X: PDB Molecule:upf0217 protein mj1640;
PDBTitle: crystal structure of duf358 protein reveals a putative spout-class2 rrna methyltransferase
42c2ejwB_
not modelled 11.9 35
PDB header:oxidoreductase
Chain: B: PDB Molecule:homoserine dehydrogenase;
PDBTitle: homoserine dehydrogenase from thermus thermophilus hb8
43c3mtjA_
not modelled 11.2 26
PDB header:oxidoreductase
Chain: A: PDB Molecule:homoserine dehydrogenase;
PDBTitle: the crystal structure of a homoserine dehydrogenase from thiobacillus2 denitrificans to 2.15a
44c6emrA_
not modelled 11.2 16
PDB header:transcription
Chain: A: PDB Molecule:pc4 and sfrs1-interacting protein,protein iws1 homolog;
PDBTitle: solution structure of the ledgf/p75 ibd - iws1 (aa 446-548) complex
45c4b1vM_
not modelled 10.8 24
PDB header:structural protein
Chain: M: PDB Molecule:phosphatase and actin regulator 1;
PDBTitle: structure of the phactr1 rpel-n domain bound to g-actin
46c4b1vN_
not modelled 10.8 24
PDB header:structural protein
Chain: N: PDB Molecule:phosphatase and actin regulator 1;
PDBTitle: structure of the phactr1 rpel-n domain bound to g-actin
47c2an7A_
not modelled 10.8 18
PDB header:dna binding protein
Chain: A: PDB Molecule:protein pard;
PDBTitle: solution structure of the bacterial antidote pard
48c2r8rB_
not modelled 10.4 48
PDB header:transferase
Chain: B: PDB Molecule:sensor protein;
PDBTitle: crystal structure of the n-terminal region (19..243) of sensor protein2 kdpd from pseudomonas syringae pv. tomato str. dc3000
49c6a6xC_
not modelled 10.2 19
PDB header:toxin
Chain: C: PDB Molecule:antitoxin maze7;
PDBTitle: the crystal structure of the mtb maze-mazf-mt9 complex
50c5mwwA_
not modelled 10.1 14
PDB header:transferase
Chain: A: PDB Molecule:rna polymerase sigma factor siga;
PDBTitle: sigma1.1 domain of sigmaa from bacillus subtilis
51c2b0tA_
not modelled 10.1 21
PDB header:oxidoreductase
Chain: A: PDB Molecule:nadp isocitrate dehydrogenase;
PDBTitle: structure of monomeric nadp isocitrate dehydrogenase
52d2outa1
not modelled 10.0 24
Fold:LEM/SAP HeH motif
Superfamily:Rho N-terminal domain-like
Family:YqbF C-terminal domain-like
53c2rbfB_
not modelled 9.6 19
PDB header:oxidoreductase/dna
Chain: B: PDB Molecule:bifunctional protein puta;
PDBTitle: structure of the ribbon-helix-helix domain of escherichia coli puta2 (puta52) complexed with operator dna (o2)
54d1rfma_
not modelled 9.4 7
Fold:L-sulfolactate dehydrogenase-like
Superfamily:L-sulfolactate dehydrogenase-like
Family:L-sulfolactate dehydrogenase-like
55d2i10a2
not modelled 9.2 11
Fold:Tetracyclin repressor-like, C-terminal domain
Superfamily:Tetracyclin repressor-like, C-terminal domain
Family:Tetracyclin repressor-like, C-terminal domain
56c2c5iT_
not modelled 9.0 22
PDB header:protein transport
Chain: T: PDB Molecule:t-snare affecting a late golgi compartment
PDBTitle: n-terminal domain of tlg1 complexed with n-terminus of2 vps51 in distorted conformation
57c6g3uA_
not modelled 8.7 23
PDB header:oxidoreductase
Chain: A: PDB Molecule:isocitrate dehydrogenase;
PDBTitle: structure of pseudomonas aeruginosa isocitrate dehydrogenase, idh
58d1qs0b1
not modelled 8.6 19
Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
59c6dzsD_
not modelled 8.5 26
PDB header:oxidoreductase
Chain: D: PDB Molecule:homoserine dehydrogenase;
PDBTitle: mycobacterial homoserine dehydrogenase thra in complex with nadp
60d1tafb_
not modelled 8.4 35
Fold:Histone-fold
Superfamily:Histone-fold
Family:TBP-associated factors, TAFs
61d1vkeb_
not modelled 8.2 20
Fold:AhpD-like
Superfamily:AhpD-like
Family:CMD-like
62c5x56A_
not modelled 7.5 20
PDB header:photosynthesis
Chain: A: PDB Molecule:photosystem ii repair protein psb27-h1, chloroplastic;
PDBTitle: crystal structure of psb27 from arabidopsis thaliana
63d1w85b1
not modelled 7.2 33
Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:Branched-chain alpha-keto acid dehydrogenase Pyr module
64c4b1uM_
not modelled 7.2 24
PDB header:structural protein
Chain: M: PDB Molecule:phosphatase and actin regulator 1;
PDBTitle: structure of the phactr1 rpel domain and rpel motif directed2 assemblies with g-actin reveal the molecular basis for actin binding3 cooperativity.
65d1y88a1
not modelled 6.8 33
Fold:SAM domain-like
Superfamily:Rad51 N-terminal domain-like
Family:Hypothetical protein AF1548, C-terminal domain
66c1rgxC_
not modelled 6.7 13
PDB header:hormone/growth factor
Chain: C: PDB Molecule:resistin;
PDBTitle: crystal structure of resisitin
67c2kmfA_
not modelled 6.7 26
PDB header:photosynthesis
Chain: A: PDB Molecule:photosystem ii 11 kda protein;
PDBTitle: solution structure of psb27 from cyanobacterial photosystem2 ii
68c2n8jB_
not modelled 6.6 40
PDB header:protein binding
Chain: B: PDB Molecule:nitric oxide synthase, endothelial;
PDBTitle: structure and 15n relaxation data of calmodulin bound to the2 endothelial nitric oxide synthase calmodulin binding domain peptide3 at physiological calcium concentration
69c3c8mA_
not modelled 6.5 21
PDB header:oxidoreductase
Chain: A: PDB Molecule:homoserine dehydrogenase;
PDBTitle: crystal structure of homoserine dehydrogenase from thermoplasma2 volcanium
70c1niwB_
not modelled 6.4 33
PDB header:signaling protein/oxidoreductase
Chain: B: PDB Molecule:nitric-oxide synthase, endothelial;
PDBTitle: crystal structure of endothelial nitric oxide synthase2 peptide bound to calmodulin
71c1niwF_
not modelled 6.4 33
PDB header:signaling protein/oxidoreductase
Chain: F: PDB Molecule:nitric-oxide synthase, endothelial;
PDBTitle: crystal structure of endothelial nitric oxide synthase2 peptide bound to calmodulin
72c1niwH_
not modelled 6.4 33
PDB header:signaling protein/oxidoreductase
Chain: H: PDB Molecule:nitric-oxide synthase, endothelial;
PDBTitle: crystal structure of endothelial nitric oxide synthase2 peptide bound to calmodulin
73c1niwD_
not modelled 6.4 33
PDB header:signaling protein/oxidoreductase
Chain: D: PDB Molecule:nitric-oxide synthase, endothelial;
PDBTitle: crystal structure of endothelial nitric oxide synthase2 peptide bound to calmodulin
74c5zwo9_
not modelled 6.3 47
PDB header:splicing
Chain: 9: PDB Molecule:pre-mrna-splicing factor spp381;
PDBTitle: cryo-em structure of the yeast b complex at average resolution of 3.92 angstrom
75c6hs6E_
not modelled 6.2 19
PDB header:transport protein
Chain: E: PDB Molecule:type vi secretion protein impa;
PDBTitle: c-terminal domain of the tssa component of the type vi secretion2 system from burkholderia cenocepacia
76d2csba3
not modelled 6.2 44
Fold:SAM domain-like
Superfamily:RuvA domain 2-like
Family:Topoisomerase V repeat domain
77c5t9jB_
not modelled 6.2 39
PDB header:hydrolase
Chain: B: PDB Molecule:flap endonuclease gen homolog 1;
PDBTitle: crystal structure of human gen1 in complex with holliday junction dna2 in the upper interface
78c4d7xA_
not modelled 6.1 16
PDB header:transcription
Chain: A: PDB Molecule:mediator of rna polymerase ii transcription subunit 15;
PDBTitle: solution structure of the mediator gall11 kix domain of c.2 glabrata
79c6h3pB_
not modelled 6.0 18
PDB header:plant protein
Chain: B: PDB Molecule:chorismate mutase;
PDBTitle: crystal structure of the cytoplasmic chorismate mutase from zea mays
80c6fpgG_
not modelled 6.0 14
PDB header:cell invasion
Chain: G: PDB Molecule:chromosome 16, whole genome shotgun sequence;
PDBTitle: structure of the ustilago maydis chorismate mutase 1 in complex with a2 zea mays kiwellin
81c5avoA_
not modelled 5.9 47
PDB header:oxidoreductase
Chain: A: PDB Molecule:homoserine dehydrogenase;
PDBTitle: crystal structure of the reduced form of homoserine dehydrogenase from2 sulfolobus tokodaii.
82c6m7fB_
not modelled 5.7 28
PDB header:lyase
Chain: B: PDB Molecule:cucumene synthase;
PDBTitle: wild-type cucumene synthase
83c3mkqB_
not modelled 5.6 39
PDB header:transport protein
Chain: B: PDB Molecule:coatomer subunit alpha;
PDBTitle: crystal structure of yeast alpha/betaprime-cop subcomplex of the copi2 vesicular coat
84d2id3a2
not modelled 5.6 20
Fold:Tetracyclin repressor-like, C-terminal domain
Superfamily:Tetracyclin repressor-like, C-terminal domain
Family:Tetracyclin repressor-like, C-terminal domain
85d1ebfa2
not modelled 5.6 25
Fold:FwdE/GAPDH domain-like
Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family:Homoserine dehydrogenase-like
86c3wa8B_
not modelled 5.6 6
PDB header:rna binding protein
Chain: B: PDB Molecule:crispr-associated protein, cse2 family;
PDBTitle: crystal structure of m. ruber casb
87c4aaiB_
not modelled 5.6 18
PDB header:viral protein
Chain: B: PDB Molecule:orf e73;
PDBTitle: thermostable protein from hyperthermophilic virus ssv-rh
88c4a1qB_
not modelled 5.6 18
PDB header:viral protein
Chain: B: PDB Molecule:orf e73;
PDBTitle: solution structure of e73 protein from sulfolobus spindle-2 shaped virus ragged hills, a hyperthermophilic3 crenarchaeal virus from yellowstone national park
89d1q9ja2
not modelled 5.4 19
Fold:CoA-dependent acyltransferases
Superfamily:CoA-dependent acyltransferases
Family:NRPS condensation domain (amide synthase)
90d2ve8a1
not modelled 5.4 17
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:FtsK C-terminal domain-like
91c1rrbA_
not modelled 5.3 21
PDB header:transferase
Chain: A: PDB Molecule:raf proto-oncogene serine/threonine-protein
PDBTitle: the ras-binding domain of raf-1 from rat, nmr, 1 structure
92d1rfxa_
not modelled 5.2 13
Fold:Resistin
Superfamily:Resistin
Family:Resistin

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