Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD1222_(-)_1365350_1365814
DateWed Jul 31 22:05:31 BST 2019
Unique Job ID44f48ff21c6584d6
SequenceMADPGSVGHV ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:46.422 Y:51.192 Z:39.241
Model (left) based on template c5wuqD_
Top template information
PDB header:metal binding protein
Chain: D: PDB Molecule:anti-sigma-w factor rsiw;
PDBTitle: crystal structure of sigw in complex with its anti-sigma rsiw, a zinc2 binding form
Confidence and coverage
Confidence: 99.4% Coverage: 40%
62 residues ( 40% of your sequence) have been modelled with 99.4% confidence by the single highest scoring template.
Additional confident templates have been detected (see Domain analysis) which cover other regions of your sequence.
94 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
1c5wuqD_
99.4 15
PDB header:metal binding protein
Chain: D: PDB Molecule:anti-sigma-w factor rsiw;
PDBTitle: crystal structure of sigw in complex with its anti-sigma rsiw, a zinc2 binding form
2c5frhA_
99.4 14
PDB header:transcription
Chain: A: PDB Molecule:anti-sigma factor rsra;
PDBTitle: solution structure of oxidised rsra
3c3hugJ_
99.4 22
PDB header:transcription/membrane protein
Chain: J: PDB Molecule:probable conserved membrane protein;
PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl
4c2z2sD_
99.4 22
PDB header:transcription
Chain: D: PDB Molecule:anti-sigma factor chrr, transcriptional activator chrr;
PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr
5c3vdoB_
99.2 10
PDB header:dna binding protein/protein binding
Chain: B: PDB Molecule:anti-sigma-k factor rska;
PDBTitle: structure of extra-cytoplasmic function(ecf) sigma factor sigk in2 complex with its negative regulator rska from mycobacterium3 tuberculosis
6c6in7A_
98.7 15
PDB header:transcription
Chain: A: PDB Molecule:sigma factor algu negative regulatory protein;
PDBTitle: crystal structure of algu in complex with muca(cyto)
7c1or7C_
97.3 16
PDB header:transcription
Chain: C: PDB Molecule:sigma-e factor negative regulatory protein;
PDBTitle: crystal structure of escherichia coli sigmae with the cytoplasmic2 domain of its anti-sigma rsea
8d1or7c_
97.3 16
Fold:N-terminal, cytoplasmic domain of anti-sigmaE factor RseA
Superfamily:N-terminal, cytoplasmic domain of anti-sigmaE factor RseA
Family:N-terminal, cytoplasmic domain of anti-sigmaE factor RseA
9c3n6qF_
25.1 13
PDB header:oxidoreductase
Chain: F: PDB Molecule:yghz aldo-keto reductase;
PDBTitle: crystal structure of yghz from e. coli
10d2ou3a1
24.5 24
Fold:TerB-like
Superfamily:TerB-like
Family:COG3793-like
11c2jxuA_
24.3 13
PDB header:unknown function
Chain: A: PDB Molecule:terb;
PDBTitle: nmr solution structure of kp-terb, a tellurite resistance2 protein from klebsiella pneumoniae
12d1gvea_
22.8 16
Fold:TIM beta/alpha-barrel
Superfamily:NAD(P)-linked oxidoreductase
Family:Aldo-keto reductases (NADP)
13c6h0jA_
21.4 18
PDB header:protein binding
Chain: A: PDB Molecule:type i modular polyketide synthase;
PDBTitle: a1-type acp domain from module 5 of mlsa1
14c6gc1A_
20.0 20
PDB header:unknown function
Chain: A: PDB Molecule:nhl repeat-containing protein 2;
PDBTitle: crystal structure of trx-like and nhl repeat containing domains of2 human nhlrc2
15d2f8aa1
19.4 5
Fold:Thioredoxin fold
Superfamily:Thioredoxin-like
Family:Glutathione peroxidase-like
16c4tr3A_
18.2 15
PDB header:oxidoreductase
Chain: A: PDB Molecule:type iii iodothyronine deiodinase;
PDBTitle: mouse iodothyronine deiodinase 3 catalytic core, semet-labeled active2 site mutant secys->cys
17c5ze4A_
17.4 22
PDB header:lyase
Chain: A: PDB Molecule:dihydroxy-acid dehydratase, chloroplastic;
PDBTitle: the structure of holo- structure of dhad complex with [2fe-2s] cluster
18c5oynB_
16.2 15
PDB header:lyase
Chain: B: PDB Molecule:dehydratase, ilvd/edd family;
PDBTitle: crystal structure of d-xylonate dehydratase in holo-form
19c3lwaA_
15.6 35
PDB header:isomerase
Chain: A: PDB Molecule:secreted thiol-disulfide isomerase;
PDBTitle: the crystal structure of a secreted thiol-disulfide isomerase from2 corynebacterium glutamicum to 1.75a
20d1or5a_
15.1 6
Fold:Acyl carrier protein-like
Superfamily:ACP-like
Family:Acyl-carrier protein (ACP)
21d2v4ja1
not modelled 14.6 42
Fold:Ferredoxin-like
Superfamily:4Fe-4S ferredoxins
Family:Ferredoxin domains from multidomain proteins
22c3n2tA_
not modelled 14.2 16
PDB header:oxidoreductase
Chain: A: PDB Molecule:putative oxidoreductase;
PDBTitle: structure of the glycerol dehydrogenase akr11b4 from gluconobacter2 oxydans
23c2wfbA_
not modelled 13.7 38
PDB header:biosynthetic protein
Chain: A: PDB Molecule:putative uncharacterized protein orp;
PDBTitle: high resolution structure of the apo form of the orange2 protein (orp) from desulfovibrio gigas
24c2ju2A_
not modelled 13.3 41
PDB header:transferase
Chain: A: PDB Molecule:erythronolide synthase;
PDBTitle: minimized mean solution structure of the acyl carrier2 protein domain from module 2 of 6-deoxyerythronolide b3 synthase (debs)
25d1z6na1
not modelled 13.1 19
Fold:Thioredoxin fold
Superfamily:Thioredoxin-like
Family:Thioltransferase
26c4xk2A_
not modelled 12.6 23
PDB header:oxidoreductase
Chain: A: PDB Molecule:aldo/keto reductase;
PDBTitle: crystal structure of aldo-keto reductase from polaromonas sp. js666
27d1wjva1
not modelled 12.4 33
Fold:beta-beta-alpha zinc fingers
Superfamily:beta-beta-alpha zinc fingers
Family:C2HC finger
28c4fyuB_
not modelled 12.2 15
PDB header:oxidoreductase
Chain: B: PDB Molecule:thioredoxin;
PDBTitle: crystal structure of thioredoxin from wuchereria bancrofti at 2.02 angstrom
29c2kvcA_
not modelled 12.1 24
PDB header:unknown function
Chain: A: PDB Molecule:putative uncharacterized protein;
PDBTitle: solution structure of the mycobacterium tuberculosis protein rv0543c,2 a member of the duf3349 superfamily. seattle structural genomics3 center for infectious disease target mytud.17112.a
30d1i5ga_
not modelled 11.4 15
Fold:Thioredoxin fold
Superfamily:Thioredoxin-like
Family:Glutathione peroxidase-like
31c6drfA_
not modelled 11.4 17
PDB header:signaling protein
Chain: A: PDB Molecule:protein rd3;
PDBTitle: structure of human retinal degeneration 3(rd3) protein
32d2db7a1
not modelled 10.8 21
Fold:Orange domain-like
Superfamily:Orange domain-like
Family:Hairy Orange domain
33c2re2A_
not modelled 10.5 15
PDB header:oxidoreductase
Chain: A: PDB Molecule:uncharacterized protein ta1041;
PDBTitle: crystal structure of a putative iron-molybdenum cofactor (femo-co)2 dinitrogenase (ta1041m) from thermoplasma acidophilum dsm 1728 at3 1.30 a resolution
34d1jroa1
not modelled 10.4 35
Fold:CO dehydrogenase ISP C-domain like
Superfamily:CO dehydrogenase ISP C-domain like
Family:CO dehydrogenase ISP C-domain like
35c2he3A_
not modelled 10.3 5
PDB header:oxidoreductase
Chain: A: PDB Molecule:glutathione peroxidase 2;
PDBTitle: crystal structure of the selenocysteine to cysteine mutant of human2 glutathionine peroxidase 2 (gpx2)
36d1tjla2
not modelled 9.8 20
Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:Prokaryotic DksA/TraR C4-type zinc finger
37c5j84A_
not modelled 9.5 19
PDB header:lyase
Chain: A: PDB Molecule:dihydroxy-acid dehydratase;
PDBTitle: crystal structure of l-arabinonate dehydratase in holo-form
38c5m45I_
not modelled 9.4 12
PDB header:ligase
Chain: I: PDB Molecule:acetone carboxylase gamma subunit;
PDBTitle: structure of acetone carboxylase purified from xanthobacter2 autotrophicus
39c3jb9i_
not modelled 9.1 10
PDB header:rna binding protein/rna
Chain: I: PDB Molecule:small nuclear ribonucleoprotein f;
PDBTitle: cryo-em structure of the yeast spliceosome at 3.6 angstrom resolution
40d2fy6a1
not modelled 8.9 15
Fold:Thioredoxin fold
Superfamily:Thioredoxin-like
Family:Glutathione peroxidase-like
41c2hyxA_
not modelled 8.8 20
PDB header:unknown function
Chain: A: PDB Molecule:protein dipz;
PDBTitle: structure of the c-terminal domain of dipz from mycobacterium2 tuberculosis
42c2lusA_
not modelled 8.7 20
PDB header:oxidoreductase
Chain: A: PDB Molecule:thioredoxion;
PDBTitle: nmr structure of carcinoscorpius rotundicauda thioredoxin related2 protein 16 and its role in regulating transcription factor nf-kb3 activity
43c4i4dA_
not modelled 8.6 18
PDB header:biosynthetic protein
Chain: A: PDB Molecule:peptide synthetase nrps type ii-pcp;
PDBTitle: structure of blmi, a type-ii acyl-carrier-protein from streptomyces2 verticillus involved in bleomycin biosynthesis
44c4f40B_
not modelled 8.6 16
PDB header:oxidoreductase
Chain: B: PDB Molecule:prostaglandin f2-alpha synthase/d-arabinose dehydrogenase;
PDBTitle: x-ray crystal structure of apo prostaglandin f synthase from2 leishmania major friedlin
45d1s1pa_
not modelled 8.5 10
Fold:TIM beta/alpha-barrel
Superfamily:NAD(P)-linked oxidoreductase
Family:Aldo-keto reductases (NADP)
46c5hvcA_
not modelled 8.5 19
PDB header:transferase
Chain: A: PDB Molecule:type i modular polyketide synthase;
PDBTitle: solution structure of the apo state of the acyl carrier protein from2 the mlsa2 subunit of the mycolactone polyketide synthase
47d2cvba1
not modelled 8.3 10
Fold:Thioredoxin fold
Superfamily:Thioredoxin-like
Family:Glutathione peroxidase-like
48c4pq1B_
not modelled 8.1 40
PDB header:oxidoreductase
Chain: B: PDB Molecule:putative electron transport related protein;
PDBTitle: crystal structure and functional implications of a dsbf homologue from2 corynebacterium diphtheriae
49c3ewlA_
not modelled 8.0 15
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized conserved protein bf1870;
PDBTitle: crystal structure of conserved protein bf1870 of unknown function from2 bacteroides fragilis
50d1t3va_
not modelled 8.0 23
Fold:Ribonuclease H-like motif
Superfamily:Nitrogenase accessory factor-like
Family:MTH1175-like
51c2n98A_
not modelled 8.0 31
PDB header:transport protein
Chain: A: PDB Molecule:acyl carrier protein;
PDBTitle: solution structure of acyl carrier protein lipd from actinoplanes2 friuliensis
52d1o8xa_
not modelled 8.0 5
Fold:Thioredoxin fold
Superfamily:Thioredoxin-like
Family:Glutathione peroxidase-like
53c3razA_
not modelled 7.9 25
PDB header:oxidoreductase
Chain: A: PDB Molecule:thioredoxin-related protein;
PDBTitle: the crystal structure of thioredoxin-related protein from neisseria2 meningitidis serogroup b
54c5w1sM_
not modelled 7.8 24
PDB header:transferase
Chain: M: PDB Molecule:protein trar;
PDBTitle: x-ray crystal structure of escherichia coli rna polymerase and trar2 complex
55c3vthA_
not modelled 7.8 30
PDB header:transferase
Chain: A: PDB Molecule:hydrogenase maturation factor;
PDBTitle: crystal structure of full-length hypf in the phosphate- and2 nucleotide-bound form
56d1o73a_
not modelled 7.5 10
Fold:Thioredoxin fold
Superfamily:Thioredoxin-like
Family:Glutathione peroxidase-like
57c2l22A_
not modelled 7.4 19
PDB header:biosynthetic protein
Chain: A: PDB Molecule:mupirocin didomain acyl carrier protein;
PDBTitle: mupirocin didomain acp
58c4g9iA_
not modelled 7.4 30
PDB header:transferase
Chain: A: PDB Molecule:hydrogenase maturation protein hypf;
PDBTitle: crystal structure of t.kodakarensis hypf
59d2hzab1
not modelled 7.2 29
Fold:Ribbon-helix-helix
Superfamily:Ribbon-helix-helix
Family:CopG-like
60c3cynC_
not modelled 7.1 5
PDB header:oxidoreductase
Chain: C: PDB Molecule:probable glutathione peroxidase 8;
PDBTitle: the structure of human gpx8
61c4ca3A_
not modelled 7.1 28
PDB header:ribosomal protein
Chain: A: PDB Molecule:hybrid polyketide synthase-non ribosomal peptide
PDBTitle: solution structure of streptomyces virginiae vira acp5b
62c3ha9A_
not modelled 7.0 25
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized thioredoxin-like protein;
PDBTitle: the 1.7a crystal structure of a thioredoxin-like protein from2 aeropyrum pernix
63c2qtdA_
not modelled 6.9 24
PDB header:oxidoreductase
Chain: A: PDB Molecule:uncharacterized protein mj0327;
PDBTitle: crystal structure of a putative dinitrogenase (mj0327) from2 methanocaldococcus jannaschii dsm at 1.70 a resolution
64c5camC_
not modelled 6.9 4
PDB header:transcription
Chain: C: PDB Molecule:pupr protein;
PDBTitle: crystal structure of the cytoplasmic domain of the pseudomonas putida2 anti-sigma factor pupr (semet)
65d1hw6a_
not modelled 6.8 19
Fold:TIM beta/alpha-barrel
Superfamily:NAD(P)-linked oxidoreductase
Family:Aldo-keto reductases (NADP)
66d2hzaa1
not modelled 6.7 29
Fold:Ribbon-helix-helix
Superfamily:Ribbon-helix-helix
Family:CopG-like
67c3b73A_
not modelled 6.6 27
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:phih1 repressor-like protein;
PDBTitle: crystal structure of the phih1 repressor-like protein from haloarcula2 marismortui
68c2ywiA_
not modelled 6.5 10
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical conserved protein;
PDBTitle: crystal structure of uncharacterized conserved protein from2 geobacillus kaustophilus
69c2p31B_
not modelled 6.5 10
PDB header:oxidoreductase
Chain: B: PDB Molecule:glutathione peroxidase 7;
PDBTitle: crystal structure of human glutathione peroxidase 7
70d1n62a1
not modelled 6.3 20
Fold:CO dehydrogenase ISP C-domain like
Superfamily:CO dehydrogenase ISP C-domain like
Family:CO dehydrogenase ISP C-domain like
71c6nd4a_
not modelled 6.2 13
PDB header:ribosome
Chain: A: PDB Molecule:mpp10;
PDBTitle: conformational switches control early maturation of the eukaryotic2 small ribosomal subunit
72c3b3dA_
not modelled 6.2 14
PDB header:oxidoreductase
Chain: A: PDB Molecule:putative morphine dehydrogenase;
PDBTitle: b.subtilis ytbe
73d1pz1a_
not modelled 6.2 16
Fold:TIM beta/alpha-barrel
Superfamily:NAD(P)-linked oxidoreductase
Family:Aldo-keto reductases (NADP)
74c2lo2A_
not modelled 6.1 56
PDB header:transcription
Chain: A: PDB Molecule:saga-associated factor 11;
PDBTitle: solution structure of sgf11(63-99) zinc finger domain
75c3s9fA_
not modelled 6.1 15
PDB header:electron transport
Chain: A: PDB Molecule:tryparedoxin;
PDBTitle: the structure of tryparedoxin i from leishmania major
76c2bmxB_
not modelled 6.0 18
PDB header:oxidoreductase
Chain: B: PDB Molecule:alkyl hydroperoxidase c;
PDBTitle: mycobacterium tuberculosis ahpc
77c3gwnA_
not modelled 5.8 9
PDB header:oxidoreductase
Chain: A: PDB Molecule:probable fad-linked sulfhydryl oxidase r596;
PDBTitle: crystal structure of the fad binding domain from mimivirus sulfhydryl2 oxidase r596
78d2bmxa1
not modelled 5.8 20
Fold:Thioredoxin fold
Superfamily:Thioredoxin-like
Family:Glutathione peroxidase-like
79d2bj7a1
not modelled 5.7 50
Fold:Ribbon-helix-helix
Superfamily:Ribbon-helix-helix
Family:CopG-like
80c2hj3A_
not modelled 5.7 18
PDB header:oxidoreductase
Chain: A: PDB Molecule:sulfhydryl oxidase erv1p;
PDBTitle: structure of the arabidopsis thaliana erv1 thiol oxidase
81c1vbjB_
not modelled 5.6 12
PDB header:oxidoreductase
Chain: B: PDB Molecule:prostaglandin f synthase;
PDBTitle: the crystal structure of prostaglandin f synthase from trypanosoma2 brucei
82c4bmjC_
not modelled 5.6 27
PDB header:apoptosis
Chain: C: PDB Molecule:tax1-binding protein 1;
PDBTitle: structure of the ubz1and2 tandem of the ubiquitin-binding adaptor2 protein tax1bp1
83d1pyfa_
not modelled 5.6 9
Fold:TIM beta/alpha-barrel
Superfamily:NAD(P)-linked oxidoreductase
Family:Aldo-keto reductases (NADP)
84c3wbwA_
not modelled 5.5 12
PDB header:oxidoreductase
Chain: A: PDB Molecule:putative 2,5-diketo-d-gluconic acid reductase;
PDBTitle: crystal structure of gox0644 in complex with nadph
85c2yrmA_
not modelled 5.4 33
PDB header:gene regulation
Chain: A: PDB Molecule:b-cell lymphoma 6 protein;
PDBTitle: solution structure of the 1st zf-c2h2 domain from human b-2 cell lymphoma 6 protein
86c2kokA_
not modelled 5.4 6
PDB header:oxidoreductase
Chain: A: PDB Molecule:arsenate reductase;
PDBTitle: solution structure of an arsenate reductase (arsc) related protein2 from brucella melitensis. seattle structural genomics center for3 infectious disease target braba.00007.a.
87c3or5A_
not modelled 5.4 20
PDB header:oxidoreductase
Chain: A: PDB Molecule:thiol:disulfide interchange protein, thioredoxin family
PDBTitle: crystal structure of thiol:disulfide interchange protein, thioredoxin2 family protein from chlorobium tepidum tls
88d1t3ba1
not modelled 5.3 12
Fold:Thioredoxin fold
Superfamily:Thioredoxin-like
Family:DsbC/DsbG C-terminal domain-like
89d1rdua_
not modelled 5.2 36
Fold:Ribonuclease H-like motif
Superfamily:Nitrogenase accessory factor-like
Family:MTH1175-like
90c2yreA_
not modelled 5.2 44
PDB header:protein binding
Chain: A: PDB Molecule:f-box only protein 30;
PDBTitle: solution structure of the zinc finger domains (1-87) from2 human f-box only protein
91c3fkfC_
not modelled 5.2 11
PDB header:oxidoreductase
Chain: C: PDB Molecule:thiol-disulfide oxidoreductase;
PDBTitle: thiol-disulfide oxidoreductase from bacteroides fragilis nctc 9343
92c2bp1C_
not modelled 5.2 21
PDB header:oxidoreductase
Chain: C: PDB Molecule:aflatoxin b1 aldehyde reductase member 2;
PDBTitle: structure of the aflatoxin aldehyde reductase in complex with nadph
93c3krbB_
not modelled 5.2 9
PDB header:oxidoreductase
Chain: B: PDB Molecule:aldose reductase;
PDBTitle: structure of aldose reductase from giardia lamblia at 1.75a resolution
94c4nsmA_
not modelled 5.1 44
PDB header:structural protein
Chain: A: PDB Molecule:collagen-like protein sclb;
PDBTitle: crystal structure of the streptococcal collagen-like protein 22 globular domain from invasive m3-type group a streptococcus
95c3ol4B_
not modelled 5.1 16
PDB header:unknown function
Chain: B: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of a putative uncharacterized protein from2 mycobacterium smegmatis, an ortholog of rv0543c
96d1ffva1
not modelled 5.1 23
Fold:CO dehydrogenase ISP C-domain like
Superfamily:CO dehydrogenase ISP C-domain like
Family:CO dehydrogenase ISP C-domain like
97c4hbkA_
not modelled 5.1 12
PDB header:oxidoreductase
Chain: A: PDB Molecule:aldo-keto reductase family 1, member b4 (aldose reductase);
PDBTitle: structure of the aldose reductase from schistosoma japonicum

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