Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD0427c_(xthA)_516020_516895
DateTue Jul 23 14:50:50 BST 2019
Unique Job ID122738ac5df053e6
SequenceMPDGTIDGGH ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:47.316 Y:47.776 Z:44.593
Model (left) based on template c2jc4A_
Top template information
PDB header:hydrolase
Chain: A: PDB Molecule:exodeoxyribonuclease iii;
PDBTitle: 3'-5' exonuclease (nexo) from neisseria meningitidis
Confidence and coverage
Confidence:100.0% Coverage: 88%
255 residues ( 88% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
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Sequence analysis 

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Secondary structure and disorder prediction [Show] 

Domain analysis [Show] 

Detailed template information [Hide] 

 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c2jc4A_
100.0 38
PDB header:hydrolase
Chain: A: PDB Molecule:exodeoxyribonuclease iii;
PDBTitle: 3'-5' exonuclease (nexo) from neisseria meningitidis
2d1akoa_
100.0 28
Fold:DNase I-like
Superfamily:DNase I-like
Family:DNase I-like
3c2j63B_
100.0 20
PDB header:lyase
Chain: B: PDB Molecule:ap-endonuclease;
PDBTitle: crystal structure of ap endonuclease lmap from leishmania major
4c2voaB_
100.0 36
PDB header:lyase
Chain: B: PDB Molecule:exodeoxyribonuclease iii;
PDBTitle: structure of an ap endonuclease from archaeoglobus fulgidus
5c3g0rA_
100.0 23
PDB header:hydrolase/dna
Chain: A: PDB Molecule:exodeoxyribonuclease;
PDBTitle: complex of mth0212 and an 8bp dsdna with distorted ends
6c5j8nA_
100.0 23
PDB header:hydrolase
Chain: A: PDB Molecule:exodeoxyribonuclease iii;
PDBTitle: exonuclease iii homologue mm3148 from methanosarcina mazei
7c1e9nB_
100.0 28
PDB header:dna repair
Chain: B: PDB Molecule:dna-(apurinic or apyrimidinic site) lyase;
PDBTitle: a second divalent metal ion in the active site of a new crystal form2 of human apurinic/apyrimidinic endonuclease, ape1, and its3 implications for the catalytic mechanism
8c4ruwA_
100.0 21
PDB header:hydrolase
Chain: A: PDB Molecule:endonuclease/exonuclease/phosphatase;
PDBTitle: the crystal structure of endonuclease/exonuclease/phosphatase from2 beutenbergia cavernae dsm 12333
9c2jc5A_
100.0 25
PDB header:hydrolase
Chain: A: PDB Molecule:exodeoxyribonuclease;
PDBTitle: apurinic apyrimidinic (ap) endonuclease (nape) from neisseria2 meningitidis
10c5ewtA_
100.0 23
PDB header:hydrolase
Chain: A: PDB Molecule:exodeoxyribonuclease iii xth;
PDBTitle: crystal structure of exoiii endonuclease from sulfolobus islandicus
11c4f1rA_
100.0 22
PDB header:transcription regulator
Chain: A: PDB Molecule:catabolite repression control protein;
PDBTitle: structure analysis of the global metabolic regulator crc from2 pseudomonas aeruginos
12c4f1iA_
100.0 16
PDB header:hydrolase
Chain: A: PDB Molecule:5'-tyrosyl-dna phosphodiesterase;
PDBTitle: crystal structure of semet tdp2 from caenorhabditis elegans
13c5cfeA_
100.0 28
PDB header:hydrolase
Chain: A: PDB Molecule:exodeoxyribonuclease;
PDBTitle: bacillus subtilis ap endonuclease exoa
14d1hd7a_
100.0 28
Fold:DNase I-like
Superfamily:DNase I-like
Family:DNase I-like
15c4fvaD_
100.0 17
PDB header:hydrolase
Chain: D: PDB Molecule:5'-tyrosyl-dna phosphodiesterase;
PDBTitle: crystal structure of truncated caenorhabditis elegans tdp2
16c3tebA_
100.0 17
PDB header:hydrolase
Chain: A: PDB Molecule:endonuclease/exonuclease/phosphatase;
PDBTitle: endonuclease/exonuclease/phosphatase family protein from leptotrichia2 buccalis c-1013-b
17c4zkfA_
100.0 15
PDB header:hydrolase
Chain: A: PDB Molecule:2',5'-phosphodiesterase 12;
PDBTitle: crystal structure of human phosphodiesterase 12
18d1vyba_
100.0 21
Fold:DNase I-like
Superfamily:DNase I-like
Family:DNase I-like
19c4gz1B_
100.0 15
PDB header:hydrolase/dna
Chain: B: PDB Molecule:tyrosyl-dna phosphodiesterase 2;
PDBTitle: mus musculus tdp2 reaction product (5'-phosphorylated dna)-mg2+2 complex at 1.5 angstroms resolution
20c4f1hA_
100.0 16
PDB header:hydrolase/dna
Chain: A: PDB Molecule:tyrosyl-dna phosphodiesterase 2;
PDBTitle: crystal structure of tdp2 from danio rerio complexed with a single2 strand dna
21c3ngoA_
not modelled 100.0 15
PDB header:hydrolase/dna
Chain: A: PDB Molecule:ccr4-not transcription complex subunit 6-like;
PDBTitle: crystal structure of the human cnot6l nuclease domain in complex with2 poly(a) dna
22d2imqx1
not modelled 100.0 13
Fold:DNase I-like
Superfamily:DNase I-like
Family:Inositol polyphosphate 5-phosphatase (IPP5)
23c3mprB_
not modelled 100.0 18
PDB header:hydrolase
Chain: B: PDB Molecule:putative endonuclease/exonuclease/phosphatase family
PDBTitle: crystal structure of endonuclease/exonuclease/phosphatase family2 protein from bacteroides thetaiotaomicron, northeast structural3 genomics consortium target btr318a
24c3g6sA_
not modelled 100.0 20
PDB header:hydrolase
Chain: A: PDB Molecule:putative endonuclease/exonuclease/phosphatase family
PDBTitle: crystal structure of the endonuclease/exonuclease/phosphatase2 (bvu_0621) from bacteroides vulgatus. northeast structural genomics3 consortium target bvr56d
25c6bt2B_
not modelled 100.0 16
PDB header:hydrolase, rna binding protein
Chain: B: PDB Molecule:nocturnin;
PDBTitle: structure of the human nocturnin catalytic domain with bound sulfate2 anion
26c3l1wE_
not modelled 100.0 17
PDB header:structural genomics, unknown function
Chain: E: PDB Molecule:uncharacterized protein;
PDBTitle: the crystal structure of a functionally unknown conserved2 protein from enterococcus faecalis v583
27c3i46B_
not modelled 100.0 14
PDB header:toxin
Chain: B: PDB Molecule:beta-hemolysin;
PDBTitle: crystal structure of beta toxin from staphylococcus aureus f277a,2 p278a mutant with bound calcium ions
28d1wdua_
not modelled 100.0 14
Fold:DNase I-like
Superfamily:DNase I-like
Family:DNase I-like
29d1zwxa1
not modelled 100.0 13
Fold:DNase I-like
Superfamily:DNase I-like
Family:Sphingomyelin phosphodiesterase-like
30c5uvgA_
not modelled 100.0 18
PDB header:hydrolase
Chain: A: PDB Molecule:sphingomyelin phosphodiesterase 3,sphingomyelin
PDBTitle: crystal structure of the human neutral sphingomyelinase 2 (nsmase2)2 catalytic domain with insertion deleted and calcium bound
31c3wcxA_
not modelled 100.0 16
PDB header:hydrolase
Chain: A: PDB Molecule:sphingomyelinase c;
PDBTitle: crystal structure of sphingomyelinase c from streptomyces2 griseocarneus
32d2ddra1
not modelled 100.0 16
Fold:DNase I-like
Superfamily:DNase I-like
Family:Sphingomyelin phosphodiesterase-like
33c3mtcA_
not modelled 100.0 13
PDB header:hydrolase/hydrolase inhibitor
Chain: A: PDB Molecule:type ii inositol-1,4,5-trisphosphate 5-phosphatase;
PDBTitle: crystal structure of inpp5b in complex with phosphatidylinositol 4-2 phosphate
34c2ei9A_
not modelled 100.0 13
PDB header:gene regulation
Chain: A: PDB Molecule:non-ltr retrotransposon r1bmks orf2 protein;
PDBTitle: crystal structure of r1bm endonuclease domain
35c3nr8A_
not modelled 100.0 14
PDB header:hydrolase
Chain: A: PDB Molecule:phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2;
PDBTitle: crystal structure of human ship2
36c4k6lF_
not modelled 99.9 21
PDB header:toxin
Chain: F: PDB Molecule:cytolethal distending toxin subunit b homolog;
PDBTitle: structure of typhoid toxin
37d2a40b1
not modelled 99.9 16
Fold:DNase I-like
Superfamily:DNase I-like
Family:DNase I-like
38d2f1na1
not modelled 99.9 23
Fold:DNase I-like
Superfamily:DNase I-like
Family:DNase I-like
39d1sr4b_
not modelled 99.9 19
Fold:DNase I-like
Superfamily:DNase I-like
Family:DNase I-like
40c2xswB_
not modelled 99.8 12
PDB header:hydrolase
Chain: B: PDB Molecule:72 kda inositol polyphosphate 5-phosphatase;
PDBTitle: crystal structure of human inpp5e
41c6ibdA_
not modelled 99.8 12
PDB header:hydrolase
Chain: A: PDB Molecule:phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1;
PDBTitle: the phosphatase and c2 domains of human ship1
42c4cmnA_
not modelled 99.8 13
PDB header:hydrolase
Chain: A: PDB Molecule:inositol polyphosphate 5-phosphatase ocrl-1;
PDBTitle: crystal structure of ocrl in complex with a phosphate ion
43c5okmA_
not modelled 99.8 15
PDB header:hydrolase
Chain: A: PDB Molecule:phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2;
PDBTitle: crystal structure of human ship2 phosphatase-c2
44d1i9za_
not modelled 99.8 16
Fold:DNase I-like
Superfamily:DNase I-like
Family:Inositol polyphosphate 5-phosphatase (IPP5)
45c6a42A_
not modelled 99.7 14
PDB header:dna binding protein
Chain: A: PDB Molecule:rna-directed dna polymerase homolog (r1),polyubiquitin-c;
PDBTitle: r1en(5-223)-ubiquitin fusion
46d1f89a_
not modelled 53.7 19
Fold:Carbon-nitrogen hydrolase
Superfamily:Carbon-nitrogen hydrolase
Family:Nitrilase
47d1emsa2
not modelled 35.7 10
Fold:Carbon-nitrogen hydrolase
Superfamily:Carbon-nitrogen hydrolase
Family:Nitrilase
48c2vhhA_
not modelled 34.8 12
PDB header:hydrolase
Chain: A: PDB Molecule:cg3027-pa;
PDBTitle: crystal structure of a pyrimidine degrading enzyme from2 drosophila melanogaster
49c6ftqA_
not modelled 33.6 16
PDB header:hydrolase
Chain: A: PDB Molecule:beta-ureidopropionase;
PDBTitle: crystal structure of human beta-ureidopropionase (beta-alanine2 synthase) - mutant t299c
50c2vhiG_
not modelled 31.6 12
PDB header:hydrolase
Chain: G: PDB Molecule:cg3027-pa;
PDBTitle: crystal structure of a pyrimidine degrading enzyme from2 drosophila melanogaster
51c4hh3C_
not modelled 31.0 11
PDB header:flavoprotein/transcription
Chain: C: PDB Molecule:appa protein;
PDBTitle: structure of the appa-ppsr2 core complex from rb. sphaeroides
52c5zfqA_
not modelled 30.5 26
PDB header:transport protein
Chain: A: PDB Molecule:twitching motility pilus retraction protein;
PDBTitle: crystal structure of pilt-4, a retraction atpase motor of type iv2 pilus , from geobacter sulfurreducens
53c3hkxA_
not modelled 29.6 15
PDB header:hydrolase
Chain: A: PDB Molecule:amidase;
PDBTitle: crystal structure analysis of an amidase from nesterenkonia sp.
54d3bula2
not modelled 29.2 7
Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
55c5h8lM_
not modelled 27.6 16
PDB header:hydrolase
Chain: M: PDB Molecule:n-carbamoylputrescine amidohydrolase;
PDBTitle: crystal structure of medicago truncatula n-carbamoylputrescine2 amidohydrolase (mtcpa) c158s mutant in complex with putrescine
56d1g6oa_
not modelled 25.5 15
Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
57d1uf5a_
not modelled 24.8 19
Fold:Carbon-nitrogen hydrolase
Superfamily:Carbon-nitrogen hydrolase
Family:Carbamilase
58c5ul4A_
not modelled 21.7 16
PDB header:metal binding protein
Chain: A: PDB Molecule:oxsb protein;
PDBTitle: structure of cobalamin-dependent s-adenosylmethionine radical enzyme2 oxsb with aqua-cobalamin and s-adenosylmethionine bound
59c2gzaB_
not modelled 21.2 9
PDB header:hydrolase
Chain: B: PDB Molecule:type iv secretion system protein virb11;
PDBTitle: crystal structure of the virb11 atpase from the brucella suis type iv2 secretion system in complex with sulphate
60c3ilvA_
not modelled 19.3 19
PDB header:ligase
Chain: A: PDB Molecule:glutamine-dependent nad(+) synthetase;
PDBTitle: crystal structure of a glutamine-dependent nad(+) synthetase2 from cytophaga hutchinsonii
61c3jvvA_
not modelled 19.2 20
PDB header:atp binding protein
Chain: A: PDB Molecule:twitching mobility protein;
PDBTitle: crystal structure of p. aeruginosa pilt with bound amp-pcp
62c4kssC_
not modelled 18.7 23
PDB header:protein transport
Chain: C: PDB Molecule:type ii secretion system protein e, hemolysin-coregulated
PDBTitle: crystal structure of vibrio cholerae atpase gspse hexamer
63c2w1vA_
not modelled 17.6 16
PDB header:hydrolase
Chain: A: PDB Molecule:nitrilase homolog 2;
PDBTitle: crystal structure of mouse nitrilase-2 at 1.4a resolution
64c1y80A_
not modelled 16.5 15
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:predicted cobalamin binding protein;
PDBTitle: structure of a corrinoid (factor iiim)-binding protein from moorella2 thermoacetica
65c3wuyA_
not modelled 16.5 14
PDB header:hydrolase
Chain: A: PDB Molecule:nitrilase;
PDBTitle: crystal structure of nit6803
66c6gebK_
not modelled 16.1 10
PDB header:hydrolase
Chain: K: PDB Molecule:dotb;
PDBTitle: x-ray structure of the legionella pneumophila atpase dotb
67c2i2xD_
not modelled 15.3 19
PDB header:transferase
Chain: D: PDB Molecule:methyltransferase 1;
PDBTitle: crystal structure of methanol:cobalamin methyltransferase complex2 mtabc from methanosarcina barkeri
68d1p9ra_
not modelled 13.1 23
Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:RecA protein-like (ATPase-domain)
69c4phtC_
not modelled 13.0 23
PDB header:protein transport
Chain: C: PDB Molecule:general secretory pathway protein e;
PDBTitle: atpase gspe in complex with the cytoplasmic domain of gspl from the2 vibrio vulnificus type ii secretion system
70c3n05B_
not modelled 12.9 22
PDB header:ligase
Chain: B: PDB Molecule:nh(3)-dependent nad(+) synthetase;
PDBTitle: crystal structure of nh3-dependent nad+ synthetase from streptomyces2 avermitilis
71d1xrsb1
not modelled 12.5 13
Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
72c4hcwC_
not modelled 12.2 19
PDB header:transferase
Chain: C: PDB Molecule:thiaminase-i;
PDBTitle: structure of a eukaryotic thiaminase-i
73c2yxbA_
not modelled 11.3 26
PDB header:isomerase
Chain: A: PDB Molecule:coenzyme b12-dependent mutase;
PDBTitle: crystal structure of the methylmalonyl-coa mutase alpha-subunit from2 aeropyrum pernix
74c1bmtB_
not modelled 10.9 7
PDB header:methyltransferase
Chain: B: PDB Molecule:methionine synthase;
PDBTitle: how a protein binds b12: a 3.o angstrom x-ray structure of2 the b12-binding domains of methionine synthase
75c5it5B_
not modelled 10.5 21
PDB header:transport protein
Chain: B: PDB Molecule:atp binding motif-containing protein pilf;
PDBTitle: thermus thermophilus pilb core atpase region
76c4ryaA_
not modelled 10.5 24
PDB header:transport protein
Chain: A: PDB Molecule:abc transporter substrate binding protein (sorbitol);
PDBTitle: crystal structure of abc transporter solute binding protein avi_35672 from agrobacterium vitis s4, target efi-510645, with bound d-mannitol
77d2yvta1
not modelled 10.3 12
Fold:Metallo-dependent phosphatases
Superfamily:Metallo-dependent phosphatases
Family:TT1561-like
78c5fl3A_
not modelled 10.2 23
PDB header:transport protein
Chain: A: PDB Molecule:pili retraction protein pilt;
PDBTitle: pilt2 from thermus thermophilus
79c4hg3C_
not modelled 10.2 23
PDB header:hydrolase
Chain: C: PDB Molecule:probable hydrolase nit2;
PDBTitle: structural insights into yeast nit2: wild-type yeast nit2 in complex2 with alpha-ketoglutarate
80c3ezxA_
not modelled 9.8 4
PDB header:transferase
Chain: A: PDB Molecule:monomethylamine corrinoid protein 1;
PDBTitle: structure of methanosarcina barkeri monomethylamine2 corrinoid protein
81c5fyoA_
not modelled 9.6 27
PDB header:hydrolase
Chain: A: PDB Molecule:phosphoinositol-specific phospholipase c;
PDBTitle: calcium-dependent phosphoinositol-specific phospholipase c from a2 gram-negative bacterium, pseudomonas sp, apo form, crystal form 1
82c2gszE_
not modelled 9.0 26
PDB header:protein transport
Chain: E: PDB Molecule:twitching motility protein pilt;
PDBTitle: structure of a. aeolicus pilt with 6 monomers per asymmetric unit
83c1xrsB_
not modelled 8.6 13
PDB header:isomerase
Chain: B: PDB Molecule:d-lysine 5,6-aminomutase beta subunit;
PDBTitle: crystal structure of lysine 5,6-aminomutase in complex with plp,2 cobalamin, and 5'-deoxyadenosine
84c4jgiB_
not modelled 8.6 11
PDB header:protein binding
Chain: B: PDB Molecule:putative uncharacterized protein;
PDBTitle: 1.5 angstrom crystal structure of a novel cobalamin-binding protein2 from desulfitobacterium hafniense dcb-2
85c5tshF_
not modelled 8.4 19
PDB header:atp-binding protein
Chain: F: PDB Molecule:type iv pilus biogenesis atpase pilb;
PDBTitle: pilb from geobacter metallireducens bound to amp-pnp
86c2eyuA_
not modelled 8.2 19
PDB header:protein transport
Chain: A: PDB Molecule:twitching motility protein pilt;
PDBTitle: the crystal structure of the c-terminal domain of aquifex2 aeolicus pilt
87c3nrbD_
not modelled 8.0 6
PDB header:hydrolase
Chain: D: PDB Molecule:formyltetrahydrofolate deformylase;
PDBTitle: crystal structure of a formyltetrahydrofolate deformylase (puru,2 pp_1943) from pseudomonas putida kt2440 at 2.05 a resolution
88c6gefB_
not modelled 7.8 11
PDB header:hydrolase
Chain: B: PDB Molecule:type iv secretion system protein dotb;
PDBTitle: x-ray structure of the yersinia pseudotuberculosis atpase dotb
89c3w7bB_
not modelled 7.7 24
PDB header:hydrolase
Chain: B: PDB Molecule:formyltetrahydrofolate deformylase;
PDBTitle: crystal structure of formyltetrahydrofolate deformylase from thermus2 thermophilus hb8
90c3n0vD_
not modelled 7.6 12
PDB header:hydrolase
Chain: D: PDB Molecule:formyltetrahydrofolate deformylase;
PDBTitle: crystal structure of a formyltetrahydrofolate deformylase (pp_0327)2 from pseudomonas putida kt2440 at 2.25 a resolution
91d1ccwa_
not modelled 7.2 9
Fold:Flavodoxin-like
Superfamily:Cobalamin (vitamin B12)-binding domain
Family:Cobalamin (vitamin B12)-binding domain
92d3thia_
not modelled 7.1 27
Fold:Periplasmic binding protein-like II
Superfamily:Periplasmic binding protein-like II
Family:Phosphate binding protein-like
93c4ii7D_
not modelled 7.0 13
PDB header:hydrolase
Chain: D: PDB Molecule:flai atpase;
PDBTitle: archaellum assembly atpase flai
94c3obiC_
not modelled 6.7 6
PDB header:hydrolase
Chain: C: PDB Molecule:formyltetrahydrofolate deformylase;
PDBTitle: crystal structure of a formyltetrahydrofolate deformylase (np_949368)2 from rhodopseudomonas palustris cga009 at 1.95 a resolution
95d1xm7a_
not modelled 6.6 6
Fold:Metallo-dependent phosphatases
Superfamily:Metallo-dependent phosphatases
Family:Hypothetical protein aq 1666
96c1k98A_
not modelled 6.6 9
PDB header:transferase
Chain: A: PDB Molecule:methionine synthase;
PDBTitle: adomet complex of meth c-terminal fragment
97c3o1lB_
not modelled 6.5 24
PDB header:hydrolase
Chain: B: PDB Molecule:formyltetrahydrofolate deformylase;
PDBTitle: crystal structure of a formyltetrahydrofolate deformylase (pspto_4314)2 from pseudomonas syringae pv. tomato str. dc3000 at 2.20 a resolution
98c5ji5A_
not modelled 6.4 17
PDB header:hydrolase
Chain: A: PDB Molecule:bupha.10154.a.b1;
PDBTitle: crystal structure of a histone deacetylase superfamily protein from2 burkholderia phymatumphymatum
99c3louB_
not modelled 6.3 12
PDB header:hydrolase
Chain: B: PDB Molecule:formyltetrahydrofolate deformylase;
PDBTitle: crystal structure of formyltetrahydrofolate deformylase (yp_105254.1)2 from burkholderia mallei atcc 23344 at 1.90 a resolution

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