Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD3051c_(nrdE)_3412096_3414177
DateThu Aug 8 16:20:22 BST 2019
Unique Job IDeb88bc9a0624d2b7
SequenceMLNLYDADGK ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:65.768 Y:75.740 Z:75.263
Model (left) based on template c1pemA_
Top template information
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase 2 alpha
PDBTitle: ribonucleotide reductase protein r1e from salmonella2 typhimurium
Confidence and coverage
Confidence:100.0% Coverage: 97%
673 residues ( 97% 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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Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1pemA_



100.0 72
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase 2 alpha
PDBTitle: ribonucleotide reductase protein r1e from salmonella2 typhimurium
2c6cgmA_



100.0 48
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase;
PDBTitle: x-ray crystal structure of bacillus subtilis ribonucleotide reductase2 nrde alpha subunit (nucleotide free)
3c3r1rB_



100.0 24
PDB header:complex (oxidoreductase/peptide)
Chain: B: PDB Molecule:ribonucleotide reductase r1 protein;
PDBTitle: ribonucleotide reductase r1 protein with amppnp occupying2 the activity site from escherichia coli
4c1zyzA_



100.0 27
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large chain 1;
PDBTitle: structures of yeast ribonucloetide reductase i
5c2wghA_



100.0 27
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large
PDBTitle: human ribonucleotide reductase r1 subunit (rrm1) in complex2 with datp and mg.
6c2cvuA_



100.0 27
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large chain
PDBTitle: structures of yeast ribonucleotide reductase i
7c5im3A_



100.0 27
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase;
PDBTitle: crystal structure of the class i ribonucleotide reductase from2 pseudomonas aeruginosa in complex with datp
8c3hnfA_



100.0 28
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large subunit;
PDBTitle: crystal structure of human ribonucleotide reductase 1 bound to the2 effectors ttp and datp
9c3rsrA_



100.0 27
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase large chain 1;
PDBTitle: crystal structure of 5-nitp inhibition of yeast ribonucleotide2 reductase
10c3pawD_



100.0 28
PDB header:oxidoreductase
Chain: D: PDB Molecule:ribonucleoside-diphosphate reductase large chain 1;
PDBTitle: low resolution x-ray crystal structure of yeast rnr1p with datp bound2 in the a-site
11c1xjeA_



100.0 28
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleotide reductase, b12-dependent;
PDBTitle: structural mechanism of allosteric substrate specificity in a2 ribonucleotide reductase: dttp-gdp complex
12d1rlra2



100.0 27
Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:R1 subunit of ribonucleotide reductase, C-terminal domain
13d1peqa2



100.0 74
Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:R1 subunit of ribonucleotide reductase, C-terminal domain
14c6dqxA_



100.0 29
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside-diphosphate reductase, alpha chain;
PDBTitle: actinobacillus ureae class id ribonucleotide reductase alpha subunit
15c6dqwB_



100.0 33
PDB header:oxidoreductase
Chain: B: PDB Molecule:ribonucleoside-diphosphate reductase, alpha chain;
PDBTitle: flavobacterium johnsoniae class id ribonucleotide reductase alpha2 subuint
16c6dqwD_



100.0 35
PDB header:oxidoreductase
Chain: D: PDB Molecule:ribonucleoside-diphosphate reductase, alpha chain;
PDBTitle: flavobacterium johnsoniae class id ribonucleotide reductase alpha2 subuint
17d1l1la_



100.0 19
Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:B12-dependent (class II) ribonucleotide reductase
18d1peqa1



100.0 64
Fold:R1 subunit of ribonucleotide reductase, N-terminal domain
Superfamily:R1 subunit of ribonucleotide reductase, N-terminal domain
Family:R1 subunit of ribonucleotide reductase, N-terminal domain
19d1rlra1



100.0 11
Fold:R1 subunit of ribonucleotide reductase, N-terminal domain
Superfamily:R1 subunit of ribonucleotide reductase, N-terminal domain
Family:R1 subunit of ribonucleotide reductase, N-terminal domain
20c4u3eA_



98.2 13
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribonucleoside triphosphate reductase;
PDBTitle: anaerobic ribonucleotide reductase
21c1hk8A_



not modelled 97.4 15
PDB header:oxidoreductase
Chain: A: PDB Molecule:anaerobic ribonucleotide-triphosphate reductase;
PDBTitle: structural basis for allosteric substrate specificity regulation in2 class iii ribonucleotide reductases: nrdd in complex with dgtp
22d1hk8a_



not modelled 97.4 15
Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:Class III anaerobic ribonucleotide reductase NRDD subunit
23c1h7bA_



not modelled 97.1 18
PDB header:oxidoreductase
Chain: A: PDB Molecule:anaerobic ribonucleotide-triphosphate reductase large
PDBTitle: structural basis for allosteric substrate specificity regulation in2 class iii ribonucleotide reductases, native nrdd
24c3pg6D_



not modelled 59.7 22
PDB header:ligase
Chain: D: PDB Molecule:e3 ubiquitin-protein ligase dtx3l;
PDBTitle: the carboxyl terminal domain of human deltex 3-like
25d1h16a_



not modelled 57.7 15
Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
26d2okqa1



not modelled 51.4 22
Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:YbaA-like
27c3vndD_



not modelled 47.1 13
PDB header:lyase
Chain: D: PDB Molecule:tryptophan synthase alpha chain;
PDBTitle: crystal structure of tryptophan synthase alpha-subunit from the2 psychrophile shewanella frigidimarina k14-2
28c4ov9A_



not modelled 41.6 14
PDB header:transferase
Chain: A: PDB Molecule:isopropylmalate synthase;
PDBTitle: structure of isopropylmalate synthase binding with alpha-2 isopropylmalate
29c2okqB_



not modelled 41.1 22
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:hypothetical protein ybaa;
PDBTitle: crystal structure of unknown conserved ybaa protein from shigella2 flexneri
30c5ey5A_



not modelled 39.7 16
PDB header:lyase
Chain: A: PDB Molecule:lbcats-a;
PDBTitle: lbcats
31d1h3ob_



not modelled 36.3 9
Fold:Histone-fold
Superfamily:Histone-fold
Family:TBP-associated factors, TAFs
32c3p9aI_



not modelled 35.9 11
PDB header:dna binding protein
Chain: I: PDB Molecule:dna-packaging protein gp3;
PDBTitle: an atomic view of the nonameric small terminase subunit of2 bacteriophage p22
33d2ccqa1



not modelled 31.9 12
Fold:PUG domain-like
Superfamily:PUG domain-like
Family:PUG domain
34c5udbB_



not modelled 29.5 11
PDB header:replication
Chain: B: PDB Molecule:origin recognition complex subunit 2;
PDBTitle: structural basis of mcm2-7 replicative helicase loading by orc-cdc62 and cdt1
35c4juyB_



not modelled 27.4 8
PDB header:unknown function
Chain: B: PDB Molecule:e3 ubiquitin-protein ligase rnf31;
PDBTitle: crystal structure of the pub domain of e3 ubiquitin ligase rnf31
36d1ic8a2



not modelled 27.1 17
Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:POU-specific domain
37d1geqa_



not modelled 26.3 10
Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
38c6hqaK_



not modelled 25.8 10
PDB header:transcription
Chain: K: PDB Molecule:subunit (61/68 kda) of tfiid and saga complexes;
PDBTitle: molecular structure of promoter-bound yeast tfiid
39d1qhma_



not modelled 25.8 15
Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
40c5kzmA_



not modelled 24.3 12
PDB header:lyase
Chain: A: PDB Molecule:tryptophan synthase alpha chain;
PDBTitle: crystal structure of tryptophan synthase alpha-beta chain complex from2 francisella tularensis
41c3u3iA_



not modelled 23.9 24
PDB header:rna binding protein
Chain: A: PDB Molecule:nucleocapsid protein;
PDBTitle: a rna binding protein from crimean-congo hemorrhagic fever virus
42d1v93a_



not modelled 21.8 17
Fold:TIM beta/alpha-barrel
Superfamily:FAD-linked oxidoreductase
Family:Methylenetetrahydrofolate reductase
43c5tchG_



not modelled 21.4 14
PDB header:lyase
Chain: G: PDB Molecule:tryptophan synthase alpha chain;
PDBTitle: crystal structure of tryptophan synthase from m. tuberculosis -2 ligand-free form, trpa-g66v mutant
44c4xgcB_



not modelled 18.7 15
PDB header:dna binding protein
Chain: B: PDB Molecule:origin recognition complex subunit 2;
PDBTitle: crystal structure of the eukaryotic origin recognition complex
45c6fosO_



not modelled 17.5 10
PDB header:photosynthesis
Chain: O: PDB Molecule:psam;
PDBTitle: cyanidioschyzon merolae photosystem i
46c5vodD_



not modelled 17.3 19
PDB header:viral protein/immune system
Chain: D: PDB Molecule:envelope glycoprotein ul130;
PDBTitle: crystal structure of hcmv pentamer in complex with neutralizing2 antibody 9i6
47c3navB_



not modelled 15.8 11
PDB header:lyase
Chain: B: PDB Molecule:tryptophan synthase alpha chain;
PDBTitle: crystal structure of an alpha subunit of tryptophan synthase from2 vibrio cholerae o1 biovar el tor str. n16961
48c5ze4A_



not modelled 15.6 18
PDB header:lyase
Chain: A: PDB Molecule:dihydroxy-acid dehydratase, chloroplastic;
PDBTitle: the structure of holo- structure of dhad complex with [2fe-2s] cluster
49d1msza_



not modelled 15.6 14
Fold:IF3-like
Superfamily:R3H domain
Family:R3H domain
50c1mszA_



not modelled 15.6 14
PDB header:dna binding protein
Chain: A: PDB Molecule:dna-binding protein smubp-2;
PDBTitle: solution structure of the r3h domain from human smubp-2
51d2d5ua1



not modelled 15.1 12
Fold:PUG domain-like
Superfamily:PUG domain-like
Family:PUG domain
52c2xrgA_



not modelled 14.7 17
PDB header:hydrolase
Chain: A: PDB Molecule:ectonucleotide pyrophosphatase/phosphodiesterase family
PDBTitle: crystal structure of autotaxin (enpp2) in complex with the2 ha155 boronic acid inhibitor
53d1vmha_



not modelled 14.7 13
Fold:YjbQ-like
Superfamily:YjbQ-like
Family:YjbQ-like
54d1vmfa_



not modelled 14.4 6
Fold:YjbQ-like
Superfamily:YjbQ-like
Family:YjbQ-like
55d1vmja_



not modelled 14.1 23
Fold:YjbQ-like
Superfamily:YjbQ-like
Family:YjbQ-like
56c3kowH_



not modelled 13.8 23
PDB header:metal binding protein
Chain: H: PDB Molecule:d-ornithine aminomutase s component;
PDBTitle: crystal structure of ornithine 4,5 aminomutase backsoaked complex
57d1td6a_



not modelled 13.7 23
Fold:Hypothetical protein MPN330
Superfamily:Hypothetical protein MPN330
Family:Hypothetical protein MPN330
58c4pfxA_



not modelled 13.6 10
PDB header:transferase
Chain: A: PDB Molecule:putative glycosyltransferase (galt1);
PDBTitle: the highly conserved domain of unknown function 1792 has a distinct2 glycosyltransferase fold
59d1vkna2



not modelled 13.4 14
Fold:FwdE/GAPDH domain-like
Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family:GAPDH-like
60c2i3eA_



not modelled 13.1 17
PDB header:hydrolase
Chain: A: PDB Molecule:g-rich;
PDBTitle: solution structure of catalytic domain of goldfish rich2 protein
61c5v4aB_



not modelled 12.5 16
PDB header:transferase
Chain: B: PDB Molecule:glycosyltransferase (duf1792);
PDBTitle: a new glycosyltransferase (duf1792) from streptococcus sanguinis
62d1v74b_



not modelled 12.4 16
Fold:Four-helical up-and-down bundle
Superfamily:Colicin D immunity protein
Family:Colicin D immunity protein
63c3rcqA_



not modelled 12.0 17
PDB header:oxidoreductase
Chain: A: PDB Molecule:aspartyl/asparaginyl beta-hydroxylase;
PDBTitle: crystal structure of human aspartate beta-hydroxylase isoform a
64c2p6hB_



not modelled 11.8 16
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:hypothetical protein;
PDBTitle: crystal structure of hypothetical protein ape1520 from aeropyrum2 pernix k1
65c2v1nA_



not modelled 11.7 19
PDB header:nuclear protein
Chain: A: PDB Molecule:protein kin homolog;
PDBTitle: solution structure of the region 51-160 of human kin172 reveals a winged helix fold
66c2xr9A_



not modelled 11.4 20
PDB header:hydrolase
Chain: A: PDB Molecule:ectonucleotide pyrophosphatase/phosphodiesterase family
PDBTitle: crystal structure of autotaxin (enpp2)
67c5c8hA_



not modelled 11.4 30
PDB header:replication
Chain: A: PDB Molecule:origin recognition complex subunit 2;
PDBTitle: crystal structure of orc2 c-terminal domain
68c4b56A_



not modelled 11.2 20
PDB header:hydrolase
Chain: A: PDB Molecule:ectonucleotide pyrophosphatase/phosphodiesterase family
PDBTitle: structure of ectonucleotide pyrophosphatase-phosphodiesterase-12 (npp1)
69c5jqyA_



not modelled 11.1 17
PDB header:oxidoreductase
Chain: A: PDB Molecule:aspartyl/asparaginyl beta-hydroxylase;
PDBTitle: aspartyl/asparaginyl beta-hydroxylase (asph)oxygenase and tpr domains2 in complex with manganese, n-oxalylglycine and factor x substrate3 peptide fragment(39mer-4ser)
70c5ym0A_



not modelled 10.5 18
PDB header:lyase
Chain: A: PDB Molecule:dihydroxy-acid dehydratase, chloroplastic;
PDBTitle: the crystal structure of dhad
71c3oiyB_



not modelled 10.4 18
PDB header:isomerase
Chain: B: PDB Molecule:reverse gyrase helicase domain;
PDBTitle: helicase domain of reverse gyrase from thermotoga maritima
72d1vpha_



not modelled 10.4 11
Fold:YjbQ-like
Superfamily:YjbQ-like
Family:YjbQ-like
73c5ujmB_



not modelled 10.2 30
PDB header:replication
Chain: B: PDB Molecule:origin recognition complex subunit 2;
PDBTitle: structure of the active form of human origin recognition complex and2 its atpase motor module
74c5v89A_



not modelled 10.0 21
PDB header:ligase / protein binding
Chain: A: PDB Molecule:dcn1-like protein 4;
PDBTitle: structure of dcn4 pony domain bound to cul1 whb
75c3ty3A_



not modelled 10.0 20
PDB header:oxidoreductase
Chain: A: PDB Molecule:probable homoisocitrate dehydrogenase;
PDBTitle: crystal structure of homoisocitrate dehydrogenase from2 schizosaccharomyces pombe bound to glycyl-glycyl-glycine
76c3pe0B_



not modelled 9.9 36
PDB header:structural protein
Chain: B: PDB Molecule:plectin;
PDBTitle: structure of the central region of the plakin domain of plectin
77c5i2gB_



not modelled 9.9 20
PDB header:lyase
Chain: B: PDB Molecule:diol dehydratase;
PDBTitle: 1,2-propanediol dehydration in roseburia inulinivorans; structural2 basis for substrate and enantiomer selectivity
78c2p6cB_



not modelled 9.9 13
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:aq_2013 protein;
PDBTitle: crystal structure of hypothetical protein aq_2013 from aquifex2 aeolicus vf5.
79c5j84A_



not modelled 9.8 19
PDB header:lyase
Chain: A: PDB Molecule:dihydroxy-acid dehydratase;
PDBTitle: crystal structure of l-arabinonate dehydratase in holo-form
80c2l09A_



not modelled 9.6 8
PDB header:oxidoreductase
Chain: A: PDB Molecule:asr4154 protein;
PDBTitle: solution nmr structure of protein asr4154 from nostoc sp. pcc71202 northeast structural genomics consortium target id nsr143
81d2d0ob1



not modelled 9.4 19
Fold:Anticodon-binding domain-like
Superfamily:B12-dependent dehydatase associated subunit
Family:Dehydratase-reactivating factor beta subunit
82c3h1yA_



not modelled 9.3 9
PDB header:isomerase
Chain: A: PDB Molecule:mannose-6-phosphate isomerase;
PDBTitle: crystal structure of mannose 6-phosphate isomerase from2 salmonella typhimurium bound to substrate (f6p)and metal3 atom (zn)
83c5xgqB_



not modelled 9.0 10
PDB header:ligase
Chain: B: PDB Molecule:methionine-trna ligase;
PDBTitle: crystal structure of apo form (free-state) mycobacterium tuberculosis2 methionyl-trna synthetase
84c3q7cA_



not modelled 8.9 15
PDB header:hydrolase
Chain: A: PDB Molecule:nucleoprotein;
PDBTitle: exonuclease domain of lassa virus nucleoprotein bound to manganese
85d2b4va2



not modelled 8.9 33
Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:RNA editing terminal uridyl transferase 2, RET2, catalytic domain
86c5wqlC_



not modelled 8.8 15
PDB header:protein binding/signaling protein/hydrol
Chain: C: PDB Molecule:tail-specific protease;
PDBTitle: structure of a pdz-protease bound to a substrate-binding adaptor
87c4cx8B_



not modelled 8.7 50
PDB header:viral protein
Chain: B: PDB Molecule:pseudorabies virus protease;
PDBTitle: monomeric pseudorabies virus protease pul26n at 2.5 a resolution
88d1vkia_



not modelled 8.6 7
Fold:YbaK/ProRS associated domain
Superfamily:YbaK/ProRS associated domain
Family:YbaK/ProRS associated domain
89c2c1fA_



not modelled 8.5 24
PDB header:hydrolase
Chain: A: PDB Molecule:bifunctional endo-1,4-beta-xylanase a;
PDBTitle: the structure of the family 11 xylanase from neocallimastix2 patriciarum
90c4djzH_



not modelled 8.5 31
PDB header:hydrolase/hydrolase inhibitor
Chain: H: PDB Molecule:protease inhibitor sgpi-2;
PDBTitle: catalytic fragment of masp-1 in complex with its specific inhibitor2 developed by directed evolution on sgci scaffold
91c5d9aD_



not modelled 8.2 13
PDB header:viral protein
Chain: D: PDB Molecule:polymerase acidic protein;
PDBTitle: influenza c virus rna-dependent rna polymerase - space group p212121
92c3w53A_



not modelled 8.1 12
PDB header:hydrolase
Chain: A: PDB Molecule:beta-glucosidase;
PDBTitle: crystal structure of psychrophilic beta-glucosidase bglu from2 micrococcus antarcticus
93d1j09a2



not modelled 8.1 17
Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain
94c5dmuA_



not modelled 8.0 15
PDB header:transferase
Chain: A: PDB Molecule:nhej polymerase;
PDBTitle: structure of the nhej polymerase from methanocella paludicola
95d1at3a_



not modelled 8.0 40
Fold:Herpes virus serine proteinase, assemblin
Superfamily:Herpes virus serine proteinase, assemblin
Family:Herpes virus serine proteinase, assemblin
96c3ig3A_



not modelled 7.9 22
PDB header:signaling protein, membrane protein
Chain: A: PDB Molecule:plxna3 protein;
PDBTitle: crystal structure of mouse plexin a3 intracellular domain
97c1eu1A_



not modelled 7.9 18
PDB header:oxidoreductase
Chain: A: PDB Molecule:dimethyl sulfoxide reductase;
PDBTitle: the crystal structure of rhodobacter sphaeroides dimethylsulfoxide2 reductase reveals two distinct molybdenum coordination environments.
98d1wiga2



not modelled 7.8 33
Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:LIM domain
99c2v3sB_



not modelled 7.8 12
PDB header:transferase
Chain: B: PDB Molecule:serine/threonine-protein kinase osr1;
PDBTitle: structural insights into the recognition of substrates and2 activators by the osr1 kinase

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