Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD2020c_(-)_2266429_2266728
DateMon Aug 5 13:25:12 BST 2019
Unique Job IDdc2bcfd847a5ead8
SequenceVAPGMKWAAK ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:40.215 Y:34.089 Z:47.266
Model (left) based on template c4xqkB_
Top template information
PDB header:hydrolase/dna
Chain: B: PDB Molecule:llabiii;
PDBTitle: atp-dependent type isp restriction-modification enzyme llabiii bound2 to dna
Confidence and coverage
Confidence:100.0% Coverage: 88%
87 residues ( 88% 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
1c4xqkB_



100.0 39
PDB header:hydrolase/dna
Chain: B: PDB Molecule:llabiii;
PDBTitle: atp-dependent type isp restriction-modification enzyme llabiii bound2 to dna
2c3pgvB_



53.2 13
PDB header:hydrolase
Chain: B: PDB Molecule:haloacid dehalogenase-like hydrolase;
PDBTitle: crystal structure of a haloacid dehalogenase-like hydrolase2 (kpn_04322) from klebsiella pneumoniae subsp. pneumoniae mgh 78578 at3 2.39 a resolution
3c3dnpA_



51.7 9
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:stress response protein yhax;
PDBTitle: crystal structure of stress response protein yhax from bacillus2 subtilis
4c4bndB_



45.3 13
PDB header:isomerase
Chain: B: PDB Molecule:alpha-phosphoglucomutase;
PDBTitle: structure of an atypical alpha-phosphoglucomutase similar to2 eukaryotic phosphomannomutases
5d1nrwa_



37.6 14
Fold:HAD-like
Superfamily:HAD-like
Family:Predicted hydrolases Cof
6d1nf2a_



37.4 13
Fold:HAD-like
Superfamily:HAD-like
Family:Predicted hydrolases Cof
7c3niwA_



34.3 13
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:haloacid dehalogenase-like hydrolase;
PDBTitle: crystal structure of a haloacid dehalogenase-like hydrolase from2 bacteroides thetaiotaomicron
8c3fzqA_



31.5 16
PDB header:hydrolase
Chain: A: PDB Molecule:putative hydrolase;
PDBTitle: crystal structure of putative haloacid dehalogenase-like hydrolase2 (yp_001086940.1) from clostridium difficile 630 at 2.10 a resolution
9c3gygA_



30.5 13
PDB header:hydrolase
Chain: A: PDB Molecule:ntd biosynthesis operon putative hydrolase ntdb;
PDBTitle: crystal structure of yhjk (haloacid dehalogenase-like hydrolase2 protein) from bacillus subtilis
10d1s2oa1



29.3 5
Fold:HAD-like
Superfamily:HAD-like
Family:Predicted hydrolases Cof
11d2rbka1



28.6 13
Fold:HAD-like
Superfamily:HAD-like
Family:Predicted hydrolases Cof
12c3ebnD_



24.5 19
PDB header:hydrolase
Chain: D: PDB Molecule:replicase polyprotein 1ab;
PDBTitle: a special dimerization of sars-cov main protease c-terminal2 domain due to domain-swapping
13c3d23A_



23.9 24
PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:3c-like proteinase;
PDBTitle: main protease of hcov-hku1
14c6cj0A_



23.9 11
PDB header:lyase
Chain: A: PDB Molecule:trehalose phosphatase;
PDBTitle: chromosomal trehalose-6-phosphate phosphatase from p. aeruginosa
15c3tqdA_



22.0 10
PDB header:transferase
Chain: A: PDB Molecule:3-deoxy-manno-octulosonate cytidylyltransferase;
PDBTitle: structure of the 3-deoxy-d-manno-octulosonate cytidylyltransferase2 (kdsb) from coxiella burnetii
16c1xviA_



21.9 26
PDB header:hydrolase
Chain: A: PDB Molecule:putative mannosyl-3-phosphoglycerate phosphatase;
PDBTitle: crystal structure of yedp, phosphatase-like domain protein2 from escherichia coli k12
17d1xvia_



21.9 26
Fold:HAD-like
Superfamily:HAD-like
Family:Predicted hydrolases Cof
18d2duca1



21.5 19
Fold:Trypsin-like serine proteases
Superfamily:Trypsin-like serine proteases
Family:Viral cysteine protease of trypsin fold
19c2qyhD_



21.4 13
PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:hypothetical conserved protein, gk1056;
PDBTitle: crystal structure of the hypothetical protein (gk1056) from2 geobacillus kaustophilus hta426
20c3nbmA_



20.9 14
PDB header:transferase
Chain: A: PDB Molecule:pts system, lactose-specific iibc components;
PDBTitle: the lactose-specific iib component domain structure of the2 phosphoenolpyruvate:carbohydrate phosphotransferase system (pts) from3 streptococcus pneumoniae.
21c3polA_



not modelled 20.1 5
PDB header:transferase
Chain: A: PDB Molecule:3-deoxy-manno-octulosonate cytidylyltransferase;
PDBTitle: 2.3 angstrom crystal structure of 3-deoxy-manno-octulosonate2 cytidylyltransferase (kdsb) from acinetobacter baumannii.
22c2d99A_



not modelled 19.6 32
PDB header:transcription
Chain: A: PDB Molecule:general transcription factor ii-i repeat domain-
PDBTitle: solution structure of rsgi ruh-048, a gtf2i domain in human2 cdna
23c2dzrA_



not modelled 19.0 11
PDB header:transcription
Chain: A: PDB Molecule:general transcription factor ii-i repeat domain-
PDBTitle: solution structure of rsgi ruh-067, a gtf2i domain in human2 cdna
24c2ejeA_



not modelled 18.8 14
PDB header:transcription
Chain: A: PDB Molecule:general transcription factor ii-i;
PDBTitle: solution structure of rsgi ruh-071, a gtf2i domain in human2 cdna
25c2dn5A_



not modelled 18.7 11
PDB header:transcription
Chain: A: PDB Molecule:general transcription factor ii-i repeat domain-
PDBTitle: solution structure of rsgi ruh-057, a gtf2i domain in human2 cdna
26c3okrC_



not modelled 18.4 11
PDB header:transferase
Chain: C: PDB Molecule:2-c-methyl-d-erythritol 4-phosphate cytidylyltransferase;
PDBTitle: structure of mtb apo 2-c-methyl-d-erythritol 4-phosphate2 cytidyltransferase (ispd)
27d1h7ea_



not modelled 17.9 10
Fold:Nucleotide-diphospho-sugar transferases
Superfamily:Nucleotide-diphospho-sugar transferases
Family:Cytidylytransferase
28c2e3lA_



not modelled 17.8 25
PDB header:transcription
Chain: A: PDB Molecule:transcription factor gtf2ird2 beta;
PDBTitle: solution structure of rsgi ruh-068, a gtf2i domain in human2 cdna
29c3zupB_



not modelled 17.1 13
PDB header:hydrolase
Chain: B: PDB Molecule:mannosyl-3-phosphoglycerate phosphatase;
PDBTitle: the 3-dimensional structure of mpgp from thermus2 thermophilus hb27, in complex with the alpha-3 mannosylglycerate and orthophosphate reaction products.
30d1q60a_



not modelled 17.1 11
Fold:GTF2I-like repeat
Superfamily:GTF2I-like repeat
Family:GTF2I-like repeat
31d1sv0c_



not modelled 16.9 38
Fold:SAM domain-like
Superfamily:SAM/Pointed domain
Family:Pointed domain
32c2ed2A_



not modelled 16.8 18
PDB header:transcription
Chain: A: PDB Molecule:general transcription factor ii-i;
PDBTitle: solution structure of rsgi ruh-069, a gtf2i domain in human2 cdna
33c4ys8B_



not modelled 16.3 12
PDB header:transferase
Chain: B: PDB Molecule:2-c-methyl-d-erythritol 4-phosphate cytidylyltransferase;
PDBTitle: crystal structure of 2-c-methyl-d-erythritol 4-phosphate2 cytidylyltransferase (ispd) from burkholderia thailandensis
34c2dn4A_



not modelled 15.9 14
PDB header:transcription
Chain: A: PDB Molecule:general transcription factor ii-i;
PDBTitle: solution structure of rsgi ruh-060, a gtf2i domain in human2 cdna
35c5wylC_



not modelled 15.9 45
PDB header:ribosomal protein/nuclear protein
Chain: C: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of chaetomium thermophilum utp10 n-terminal domain2 in complex with utp17 c-terminal helices
36c2dzqA_



not modelled 15.7 18
PDB header:transcription
Chain: A: PDB Molecule:general transcription factor ii-i repeat domain-
PDBTitle: solution structure of rsgi ruh-066, a gtf2i domain in human2 cdna
37c3f1cB_



not modelled 15.1 10
PDB header:transferase
Chain: B: PDB Molecule:putative 2-c-methyl-d-erythritol 4-phosphate
PDBTitle: crystal structure of 2-c-methyl-d-erythritol 4-phosphate2 cytidylyltransferase from listeria monocytogenes
38c5ubdB_



not modelled 14.6 60
PDB header:dna binding protein
Chain: B: PDB Molecule:rctb replication initiator protein;
PDBTitle: crystal structure of the n-terminal domain (domain 1) of rctb, rctb-1-2 124-l48m
39c2n8pA_



not modelled 14.3 17
PDB header:antimicrobial protein
Chain: A: PDB Molecule:lacticin q;
PDBTitle: solution structure of lacticin q
40c4zexA_



not modelled 14.2 9
PDB header:unknown function
Chain: A: PDB Molecule:pfhad1;
PDBTitle: crystal structure of pfhad1 in complex with glyceraldehyde-3-phosphate
41c1vw3D_



not modelled 14.1 17
PDB header:ribosome
Chain: D: PDB Molecule:54s ribosomal protein yml6, mitochondrial;
PDBTitle: structure of the yeast mitochondrial large ribosomal subunit
42c5e9oC_



not modelled 13.4 35
PDB header:hydrolase
Chain: C: PDB Molecule:cellulase, glycosyl hydrolase family 5, tps linker, domain
PDBTitle: spirochaeta thermophila x module - cbm64 - mutant g504a
43c6nd4M_



not modelled 13.3 27
PDB header:ribosome
Chain: M: PDB Molecule:utp10;
PDBTitle: conformational switches control early maturation of the eukaryotic2 small ribosomal subunit
44d1vgwa_



not modelled 13.2 8
Fold:Nucleotide-diphospho-sugar transferases
Superfamily:Nucleotide-diphospho-sugar transferases
Family:Cytidylytransferase
45c6hlwB_



not modelled 12.8 45
PDB header:viral protein
Chain: B: PDB Molecule:genome polyprotein;
PDBTitle: crystal structure of human acbd3 gold domain in complex with 3a2 protein of enterovirus-a71 (fusion protein)
46c2n8oA_



not modelled 12.7 18
PDB header:antimicrobial protein
Chain: A: PDB Molecule:bacteriocin aureocin a53;
PDBTitle: nmr solution structure of aureocin a53
47c1ng7A_



not modelled 12.7 45
PDB header:viral protein
Chain: A: PDB Molecule:genome polyprotein [core protein p3a];
PDBTitle: the solution structure of the soluble domain of poliovirus2 3a protein
48d1ng7a_



not modelled 12.7 45
Fold:Soluble domain of poliovirus core protein 3a
Superfamily:Soluble domain of poliovirus core protein 3a
Family:Soluble domain of poliovirus core protein 3a
49c2q6fB_



not modelled 12.2 16
PDB header:hydrolase
Chain: B: PDB Molecule:infectious bronchitis virus (ibv) main protease;
PDBTitle: crystal structure of infectious bronchitis virus (ibv) main protease2 in complex with a michael acceptor inhibitor n3
50c6hltD_



not modelled 12.2 55
PDB header:viral protein
Chain: D: PDB Molecule:genome polyprotein;
PDBTitle: crystal structure of human acbd3 gold domain in complex with 3a2 protein of rhinovirus-14 (hrv14)
51d1eyra_



not modelled 12.1 26
Fold:Nucleotide-diphospho-sugar transferases
Superfamily:Nucleotide-diphospho-sugar transferases
Family:Cytidylytransferase
52c3r4cA_



not modelled 12.1 16
PDB header:hydrolase
Chain: A: PDB Molecule:hydrolase, haloacid dehalogenase-like hydrolase;
PDBTitle: divergence of structure and function among phosphatases of the2 haloalkanoate (had) enzyme superfamily: analysis of bt1666 from3 bacteroides thetaiotaomicron
53c3u3iA_



not modelled 12.1 25
PDB header:rna binding protein
Chain: A: PDB Molecule:nucleocapsid protein;
PDBTitle: a rna binding protein from crimean-congo hemorrhagic fever virus
54d1sxea_



not modelled 12.0 26
Fold:SAM domain-like
Superfamily:SAM/Pointed domain
Family:Pointed domain
55c3zljC_



not modelled 11.7 71
PDB header:dna binding protein/dna
Chain: C: PDB Molecule:dna mismatch repair protein muts;
PDBTitle: crystal structure of full-length e.coli dna mismatch repair protein2 muts d835r mutant in complex with gt mismatched dna
56c3zljD_



not modelled 11.7 71
PDB header:dna binding protein/dna
Chain: D: PDB Molecule:dna mismatch repair protein muts;
PDBTitle: crystal structure of full-length e.coli dna mismatch repair protein2 muts d835r mutant in complex with gt mismatched dna
57c4e6fB_



not modelled 11.1 31
PDB header:unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a duf4468 family protein (bacova_04320) from2 bacteroides ovatus atcc 8483 at 1.49 a resolution
58c3tloA_



not modelled 11.1 22
PDB header:hydrolase
Chain: A: PDB Molecule:3c-like proteinase;
PDBTitle: crystal structure of hcov-nl63 3c-like protease
59c3pnnA_



not modelled 11.1 0
PDB header:transferase
Chain: A: PDB Molecule:conserved domain protein;
PDBTitle: the crystal structure of a glycosyltransferase from porphyromonas2 gingivalis w83
60c3bboG_



not modelled 10.9 23
PDB header:ribosome
Chain: G: PDB Molecule:ribosomal protein l4;
PDBTitle: homology model for the spinach chloroplast 50s subunit fitted to 9.4a2 cryo-em map of the 70s chlororibosome
61d1qwja_



not modelled 10.8 18
Fold:Nucleotide-diphospho-sugar transferases
Superfamily:Nucleotide-diphospho-sugar transferases
Family:Cytidylytransferase
62c5dxiB_



not modelled 10.7 5
PDB header:hydrolase
Chain: B: PDB Molecule:trehalose-6-phosphate phosphatase;
PDBTitle: structure of c. albicans trehalose-6-phosphate phosphatase c-terminal2 domain
63c2kadA_



not modelled 10.6 43
PDB header:membrane protein
Chain: A: PDB Molecule:transmembrane peptide of matrix protein 2;
PDBTitle: magic-angle-spinning solid-state nmr structure of influenza2 a m2 transmembrane domain
64c2kadD_



not modelled 10.6 43
PDB header:membrane protein
Chain: D: PDB Molecule:transmembrane peptide of matrix protein 2;
PDBTitle: magic-angle-spinning solid-state nmr structure of influenza2 a m2 transmembrane domain
65c2kadB_



not modelled 10.6 43
PDB header:membrane protein
Chain: B: PDB Molecule:transmembrane peptide of matrix protein 2;
PDBTitle: magic-angle-spinning solid-state nmr structure of influenza2 a m2 transmembrane domain
66c2kadC_



not modelled 10.6 43
PDB header:membrane protein
Chain: C: PDB Molecule:transmembrane peptide of matrix protein 2;
PDBTitle: magic-angle-spinning solid-state nmr structure of influenza2 a m2 transmembrane domain
67c5i8jB_



not modelled 10.3 13
PDB header:antitoxin
Chain: B: PDB Molecule:dmd discriminator of mrna degradation;
PDBTitle: crystal structure of dmd from phage rb69
68c6ifdD_



not modelled 10.1 17
PDB header:sugar binding protein
Chain: D: PDB Molecule:cmp-n-acetylneuraminate synthetase;
PDBTitle: crystal structure of cmp-n-acetylneuraminate synthetase from vibrio2 cholerae in complex with cdp and mg2+.
69d1lvoa_



not modelled 9.9 22
Fold:Trypsin-like serine proteases
Superfamily:Trypsin-like serine proteases
Family:Viral cysteine protease of trypsin fold
70c4mhvB_



not modelled 9.8 31
PDB header:transcription
Chain: B: PDB Molecule:protein c-ets-2;
PDBTitle: crystal structure of the pnt domain of human ets2
71d1u02a_



not modelled 9.6 18
Fold:HAD-like
Superfamily:HAD-like
Family:Trehalose-phosphatase
72d1sxda_



not modelled 9.5 31
Fold:SAM domain-like
Superfamily:SAM/Pointed domain
Family:Pointed domain
73d1rlma_



not modelled 9.4 9
Fold:HAD-like
Superfamily:HAD-like
Family:Predicted hydrolases Cof
74d1uhwa_



not modelled 9.3 13
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:DEP domain
75c2ynbA_



not modelled 9.1 27
PDB header:hydrolase
Chain: A: PDB Molecule:3c-like proteinase;
PDBTitle: crystal structure of the main protease of coronavirus hku4 in complex2 with a michael acceptor sg85
76c2crnA_



not modelled 9.1 43
PDB header:immune system
Chain: A: PDB Molecule:ubash3a protein;
PDBTitle: solution structure of the uba domain of human ubash3a2 protein
77c6hmvB_



not modelled 9.0 27
PDB header:viral protein
Chain: B: PDB Molecule:genome polyprotein;
PDBTitle: crystal structure of human acbd3 gold domain in complex with 3a2 protein of enterovirus-d68 (fusion protein, lvvy mutant)
78d1wzca1



not modelled 8.9 13
Fold:HAD-like
Superfamily:HAD-like
Family:Predicted hydrolases Cof
79c4aezC_



not modelled 8.7 23
PDB header:cell cycle
Chain: C: PDB Molecule:mitotic spindle checkpoint component mad3;
PDBTitle: crystal structure of mitotic checkpoint complex
80c5jqmB_



not modelled 8.5 27
PDB header:transport protein
Chain: B: PDB Molecule:protein ups1, mitochondrial,mitochondrial distribution and
PDBTitle: crystal structure of phosphatidic acid transporter ups1/mdm35 void of2 bound phospholipid from saccharomyces cerevisiae at 1.5 angstroms3 resolution
81c4jisB_



not modelled 8.5 11
PDB header:transferase
Chain: B: PDB Molecule:ribitol-5-phosphate cytidylyltransferase;
PDBTitle: crystal structure of ribitol 5-phosphate cytidylyltransferase (tari)2 from bacillus subtilis
82c2px7A_



not modelled 8.4 29
PDB header:transferase
Chain: A: PDB Molecule:2-c-methyl-d-erythritol 4-phosphate cytidylyltransferase;
PDBTitle: crystal structure of 2-c-methyl-d-erythritol 4-phosphate2 cytidylyltransferase from thermus thermophilus hb8
83c6n9gB_



not modelled 8.2 9
PDB header:signaling protein
Chain: B: PDB Molecule:regulator of g-protein signaling 7;
PDBTitle: crystal structure of rgs7-gbeta5 dimer
84c2vshB_



not modelled 8.1 20
PDB header:transferase
Chain: B: PDB Molecule:2-c-methyl-d-erythritol 4-phosphate
PDBTitle: synthesis of cdp-activated ribitol for teichoic acid2 precursors in streptococcus pneumoniae
85d2crna1



not modelled 8.1 38
Fold:RuvA C-terminal domain-like
Superfamily:UBA-like
Family:UBA domain
86d1vh3a_



not modelled 8.0 18
Fold:Nucleotide-diphospho-sugar transferases
Superfamily:Nucleotide-diphospho-sugar transferases
Family:Cytidylytransferase
87c6aklA_



not modelled 8.0 45
PDB header:protein binding
Chain: A: PDB Molecule:suppressor of ikbke 1;
PDBTitle: crystal structure of striatin3 in complex with sike1 coiled-coil2 domain
88d1eexa_



not modelled 7.9 60
Fold:TIM beta/alpha-barrel
Superfamily:Cobalamin (vitamin B12)-dependent enzymes
Family:Diol dehydratase, alpha subunit
89c6akkA_



not modelled 7.6 45
PDB header:protein binding
Chain: A: PDB Molecule:suppressor of ikbke 1;
PDBTitle: crystal structure of the second coiled-coil domain of sike1
90c4mybA_



not modelled 7.6 7
PDB header:transferase
Chain: A: PDB Molecule:2-c-methyl-d-erythritol 4-phosphate cytidylyltransferase;
PDBTitle: crystal structure of francisella tularensis 2-c-methyl-d-erythritol 4-2 phosphate cytidylyltransferase (ispd)
91c4htjA_



not modelled 7.4 18
PDB header:hydrolase
Chain: A: PDB Molecule:receptor-type tyrosine-protein phosphatase n2;
PDBTitle: crystallographic structure of the membrane-proximal ectodomain of the2 human receptor-type protein-tyrosine phosphatase phogrin at ph 4.6
92d2cpwa1



not modelled 7.4 29
Fold:RuvA C-terminal domain-like
Superfamily:UBA-like
Family:UBA domain
93c2d10G_



not modelled 7.3 56
PDB header:cell adhesion
Chain: G: PDB Molecule:ezrin-radixin-moesin binding phosphoprotein 50;
PDBTitle: crystal structure of the radixin ferm domain complexed with2 the nherf-1 c-terminal tail peptide
94c2d10E_



not modelled 7.3 56
PDB header:cell adhesion
Chain: E: PDB Molecule:ezrin-radixin-moesin binding phosphoprotein 50;
PDBTitle: crystal structure of the radixin ferm domain complexed with2 the nherf-1 c-terminal tail peptide
95c2d10F_



not modelled 7.3 56
PDB header:cell adhesion
Chain: F: PDB Molecule:ezrin-radixin-moesin binding phosphoprotein 50;
PDBTitle: crystal structure of the radixin ferm domain complexed with2 the nherf-1 c-terminal tail peptide
96c2d10H_



not modelled 7.3 56
PDB header:cell adhesion
Chain: H: PDB Molecule:ezrin-radixin-moesin binding phosphoprotein 50;
PDBTitle: crystal structure of the radixin ferm domain complexed with2 the nherf-1 c-terminal tail peptide
97c2dagA_



not modelled 7.3 29
PDB header:hydrolase
Chain: A: PDB Molecule:ubiquitin carboxyl-terminal hydrolase 5;
PDBTitle: solution structure of the first uba domain in the human2 ubiquitin specific protease 5 (isopeptidase 5)
98d1bqva_



not modelled 7.1 46
Fold:SAM domain-like
Superfamily:SAM/Pointed domain
Family:Pointed domain
99d2ffta1



not modelled 7.0 17
Fold:Intrinsically disordered proteins
Superfamily:TSP9-like
Family:TSP9-like

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