Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD3148_(nuoD)_3513335_3514657
DateThu Aug 8 16:20:33 BST 2019
Unique Job IDa2e937c1d7335efd
SequenceMTAIADSAGG ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:57.746 Y:48.954 Z:84.179
Model (left) based on template c5lc5D_
Top template information
PDB header:oxidoreductase
Chain: D: PDB Molecule:nadh dehydrogenase [ubiquinone] iron-sulfur protein 2,
PDBTitle: structure of mammalian respiratory complex i, class2
Confidence and coverage
Confidence:100.0% Coverage: 89%
391 residues ( 89% 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
1c5lc5D_
100.0 44
PDB header:oxidoreductase
Chain: D: PDB Molecule:nadh dehydrogenase [ubiquinone] iron-sulfur protein 2,
PDBTitle: structure of mammalian respiratory complex i, class2
2c6gcsC_
100.0 40
PDB header:oxidoreductase
Chain: C: PDB Molecule:49-kda protein (nucm);
PDBTitle: cryo-em structure of respiratory complex i from yarrowia lipolytica
3c6humH_
100.0 39
PDB header:proton transport
Chain: H: PDB Molecule:nad(p)h-quinone oxidoreductase subunit h;
PDBTitle: structure of the photosynthetic complex i from thermosynechococcus2 elongatus
4c6cfwL_
100.0 32
PDB header:membrane protein
Chain: L: PDB Molecule:membrane-bound hydrogenase subunit alpha;
PDBTitle: cryoem structure of a respiratory membrane-bound hydrogenase
5d2fug41
100.0 49
Fold:HydB/Nqo4-like
Superfamily:HydB/Nqo4-like
Family:Nqo4-like
6c2fug4_
100.0 49
PDB header:oxidoreductase
Chain: 4: PDB Molecule:nadh-quinone oxidoreductase chain 4;
PDBTitle: crystal structure of the hydrophilic domain of respiratory complex i2 from thermus thermophilus
7d1e3db_
100.0 22
Fold:HydB/Nqo4-like
Superfamily:HydB/Nqo4-like
Family:Nickel-iron hydrogenase, large subunit
8d1frfl_
100.0 18
Fold:HydB/Nqo4-like
Superfamily:HydB/Nqo4-like
Family:Nickel-iron hydrogenase, large subunit
9d1yq9h1
100.0 21
Fold:HydB/Nqo4-like
Superfamily:HydB/Nqo4-like
Family:Nickel-iron hydrogenase, large subunit
10c1h2aL_
100.0 23
PDB header:oxidoreductase
Chain: L: PDB Molecule:hydrogenase;
PDBTitle: single crystals of hydrogenase from desulfovibrio vulgaris
11c5aa5C_
100.0 20
PDB header:oxidoreductase
Chain: C: PDB Molecule:nife-hydrogenase large subunit, hofg;
PDBTitle: actinobacterial-type nife-hydrogenase from ralstonia eutropha h16 at2 2.85 angstrom resolution
12c2wpnB_
100.0 18
PDB header:oxidoreductase
Chain: B: PDB Molecule:periplasmic [nifese] hydrogenase, large subunit,
PDBTitle: structure of the oxidised, as-isolated nifese hydrogenase from d.2 vulgaris hildenborough
13c6ehqM_
100.0 20
PDB header:oxidoreductase
Chain: M: PDB Molecule:hydrogenase-2 large chain;
PDBTitle: e. coli hydrogenase-2 (as isolated form).
14d1cc1l_
100.0 18
Fold:HydB/Nqo4-like
Superfamily:HydB/Nqo4-like
Family:Nickel-iron hydrogenase, large subunit
15c3myrB_
100.0 21
PDB header:oxidoreductase
Chain: B: PDB Molecule:nickel-dependent hydrogenase large subunit;
PDBTitle: crystal structure of [nife] hydrogenase from allochromatium vinosum in2 its ni-a state
16c5odqF_
100.0 13
PDB header:oxidoreductase
Chain: F: PDB Molecule:methyl-viologen reducing hydrogenase, subunit a;
PDBTitle: heterodisulfide reductase / [nife]-hydrogenase complex from2 methanothermococcus thermolithotrophicus soaked with3 bromoethanesulfonate.
17c5xf9H_
100.0 15
PDB header:oxidoreductase
Chain: H: PDB Molecule:nad-reducing hydrogenase;
PDBTitle: crystal structure of nad+-reducing [nife]-hydrogenase in the air-2 oxidized state
18d1wuil1
100.0 19
Fold:HydB/Nqo4-like
Superfamily:HydB/Nqo4-like
Family:Nickel-iron hydrogenase, large subunit
19c3zfsA_
100.0 20
PDB header:oxidoreductase
Chain: A: PDB Molecule:f420-reducing hydrogenase, subunit alpha;
PDBTitle: cryo-em structure of the f420-reducing nife-hydrogenase from a2 methanogenic archaeon with bound substrate
20c3useL_
100.0 18
PDB header:oxidoreductase
Chain: L: PDB Molecule:hydrogenase-1 large chain;
PDBTitle: crystal structure of e. coli hydrogenase-1 in its as-isolated form
21c4c3oC_
not modelled 100.0 19
PDB header:oxidoreductase
Chain: C: PDB Molecule:hydrogenase-1 large subunit;
PDBTitle: structure and function of an oxygen tolerant nife hydrogenase from2 salmonella
22c5yy0A_
not modelled 100.0 15
PDB header:metal binding protein
Chain: A: PDB Molecule:cytosolic nife-hydrogenase, alpha subunit;
PDBTitle: crystal structure of the hyhl-hypa complex (form ii)
23c3r07C_
not modelled 63.6 19
PDB header:transferase
Chain: C: PDB Molecule:putative lipoate-protein ligase a subunit 2;
PDBTitle: structural analysis of an archaeal lipoylation system. a bi-partite2 lipoate protein ligase and its e2 lipoyl domain from thermoplasma3 acidophilum
24d2g40a1
not modelled 59.5 25
Fold:NagB/RpiA/CoA transferase-like
Superfamily:NagB/RpiA/CoA transferase-like
Family:YkgG-like
25c2g40A_
not modelled 59.5 25
PDB header:unknown function
Chain: A: PDB Molecule:conserved hypothetical protein;
PDBTitle: crystal structure of a duf162 family protein (dr_1909) from2 deinococcus radiodurans at 1.70 a resolution
26d1v97a4
not modelled 46.4 8
Fold:CO dehydrogenase flavoprotein C-domain-like
Superfamily:CO dehydrogenase flavoprotein C-terminal domain-like
Family:CO dehydrogenase flavoprotein C-terminal domain-like
27c5ymrB_
not modelled 33.3 18
PDB header:lyase
Chain: B: PDB Molecule:formate acetyltransferase;
PDBTitle: the crystal structure of iseg
28d1yeya2
not modelled 32.4 4
Fold:Enolase N-terminal domain-like
Superfamily:Enolase N-terminal domain-like
Family:Enolase N-terminal domain-like
29d2ntka1
not modelled 32.1 9
Fold:Ntn hydrolase-like
Superfamily:Archaeal IMP cyclohydrolase PurO
Family:Archaeal IMP cyclohydrolase PurO
30d1ffvc1
not modelled 31.0 21
Fold:CO dehydrogenase flavoprotein C-domain-like
Superfamily:CO dehydrogenase flavoprotein C-terminal domain-like
Family:CO dehydrogenase flavoprotein C-terminal domain-like
31d1r9da_
not modelled 28.5 15
Fold:PFL-like glycyl radical enzymes
Superfamily:PFL-like glycyl radical enzymes
Family:PFL-like
32c4k59A_
not modelled 26.6 55
PDB header:rna binding protein
Chain: A: PDB Molecule:rna binding protein rsmf;
PDBTitle: crystal structure of pseudomonas aeruginosa rsmf
33c1ufiD_
not modelled 25.7 40
PDB header:dna binding protein
Chain: D: PDB Molecule:major centromere autoantigen b;
PDBTitle: crystal structure of the dimerization domain of human cenp-b
34d1ufia_
not modelled 25.5 40
Fold:ROP-like
Superfamily:Dimerisation domain of CENP-B
Family:Dimerisation domain of CENP-B
35c2w3zA_
not modelled 23.6 11
PDB header:hydrolase
Chain: A: PDB Molecule:putative deacetylase;
PDBTitle: structure of a streptococcus mutans ce4 esterase
36d1jroa3
not modelled 22.4 26
Fold:CO dehydrogenase flavoprotein C-domain-like
Superfamily:CO dehydrogenase flavoprotein C-terminal domain-like
Family:CO dehydrogenase flavoprotein C-terminal domain-like
37d1vqza1
not modelled 21.5 17
Fold:SufE/NifU
Superfamily:SufE/NifU
Family:SP1160 C-terminal domain-like
38c4lqzA_
not modelled 19.8 33
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a duf4909 family protein (sav1798) from2 staphylococcus aureus subsp. aureus mu50 at 1.92 a resolution
39c5ze4A_
not modelled 19.0 15
PDB header:lyase
Chain: A: PDB Molecule:dihydroxy-acid dehydratase, chloroplastic;
PDBTitle: the structure of holo- structure of dhad complex with [2fe-2s] cluster
40c4mnoA_
not modelled 18.0 15
PDB header:translation
Chain: A: PDB Molecule:translation initiation factor 1a;
PDBTitle: crystal structure of aif1a from pyrococcus abyssi
41c2f3oB_
not modelled 17.8 17
PDB header:unknown function
Chain: B: PDB Molecule:pyruvate formate-lyase 2;
PDBTitle: crystal structure of a glycyl radical enzyme from archaeoglobus2 fulgidus
42c5j84A_
not modelled 17.5 18
PDB header:lyase
Chain: A: PDB Molecule:dihydroxy-acid dehydratase;
PDBTitle: crystal structure of l-arabinonate dehydratase in holo-form
43c5dkoA_
not modelled 16.8 18
PDB header:replication
Chain: A: PDB Molecule:cell division protein zapd;
PDBTitle: the structure of escherichia coli zapd
44d1rm6b1
not modelled 15.8 18
Fold:CO dehydrogenase flavoprotein C-domain-like
Superfamily:CO dehydrogenase flavoprotein C-terminal domain-like
Family:CO dehydrogenase flavoprotein C-terminal domain-like
45c3hrdC_
not modelled 15.5 12
PDB header:oxidoreductase
Chain: C: PDB Molecule:nicotinate dehydrogenase fad-subunit;
PDBTitle: crystal structure of nicotinate dehydrogenase
46c2w3rG_
not modelled 15.5 26
PDB header:oxidoreductase
Chain: G: PDB Molecule:xanthine dehydrogenase;
PDBTitle: crystal structure of xanthine dehydrogenase (desulfo form)2 from rhodobacter capsulatus in complex with hypoxanthine
47d1jdfa2
not modelled 14.7 9
Fold:Enolase N-terminal domain-like
Superfamily:Enolase N-terminal domain-like
Family:Enolase N-terminal domain-like
48d1u07a_
not modelled 13.8 17
Fold:TolA/TonB C-terminal domain
Superfamily:TolA/TonB C-terminal domain
Family:TonB
49c2dd9C_
not modelled 13.2 15
PDB header:luminescent protein
Chain: C: PDB Molecule:green fluorescent protein;
PDBTitle: a mutant of gfp-like protein from chiridius poppei
50d1t3qc1
not modelled 11.7 18
Fold:CO dehydrogenase flavoprotein C-domain-like
Superfamily:CO dehydrogenase flavoprotein C-terminal domain-like
Family:CO dehydrogenase flavoprotein C-terminal domain-like
51d1n62c1
not modelled 11.6 15
Fold:CO dehydrogenase flavoprotein C-domain-like
Superfamily:CO dehydrogenase flavoprotein C-terminal domain-like
Family:CO dehydrogenase flavoprotein C-terminal domain-like
52c2dgyA_
not modelled 11.5 16
PDB header:translation
Chain: A: PDB Molecule:mgc11102 protein;
PDBTitle: solution structure of the eukaryotic initiation factor 1a2 in mgc11102 protein
53d1x2ga1
not modelled 11.3 17
Fold:SufE/NifU
Superfamily:SufE/NifU
Family:SP1160 C-terminal domain-like
54c4af3D_
not modelled 11.0 13
PDB header:transferase/inhibitor
Chain: D: PDB Molecule:inner centromere protein;
PDBTitle: human aurora b kinase in complex with incenp and vx-680
55c3o6uB_
not modelled 11.0 10
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein cpe2226;
PDBTitle: crystal structure of cpe2226 protein from clostridium perfringens.2 northeast structural genomics consortium target cpr195
56c2vgpD_
not modelled 10.9 13
PDB header:transferase
Chain: D: PDB Molecule:inner centromere protein a;
PDBTitle: crystal structure of aurora b kinase in complex with a2 aminothiazole inhibitor
57c2grxC_
not modelled 10.9 17
PDB header:metal transport
Chain: C: PDB Molecule:protein tonb;
PDBTitle: crystal structure of tonb in complex with fhua, e. coli2 outer membrane receptor for ferrichrome
58c5ibyA_
not modelled 10.8 21
PDB header:ligase,transferase
Chain: A: PDB Molecule:lipoate--protein ligase;
PDBTitle: crystal structure of enterococcus faecalis lipoate-protein ligase a2 (lpla-2) in complex with lipoic acid
59c3km3B_
not modelled 10.5 28
PDB header:hydrolase
Chain: B: PDB Molecule:deoxycytidine triphosphate deaminase;
PDBTitle: crystal structure of eoxycytidine triphosphate deaminase from2 anaplasma phagocytophilum at 2.1a resolution
60c1wvtA_
not modelled 10.4 5
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein st2180;
PDBTitle: crystal structure of uncharacterized protein st2180 from sulfolobus2 tokodaii
61c5i2gB_
not modelled 10.4 14
PDB header:lyase
Chain: B: PDB Molecule:diol dehydratase;
PDBTitle: 1,2-propanediol dehydration in roseburia inulinivorans; structural2 basis for substrate and enantiomer selectivity
62d2p7ja1
not modelled 10.4 17
Fold:Profilin-like
Superfamily:Sensory domain-like
Family:YkuI C-terminal domain-like
63c6gr8B_
not modelled 10.2 13
PDB header:transferase
Chain: B: PDB Molecule:inner centromere protein;
PDBTitle: human aurkc incenp complex bound to brd-7880
64c3fa4D_
not modelled 9.5 21
PDB header:lyase
Chain: D: PDB Molecule:2,3-dimethylmalate lyase;
PDBTitle: crystal structure of 2,3-dimethylmalate lyase, a pep mutase/isocitrate2 lyase superfamily member, triclinic crystal form
65c4qamB_
not modelled 9.5 27
PDB header:signaling protein
Chain: B: PDB Molecule:x-linked retinitis pigmentosa gtpase regulator-interacting
PDBTitle: crystal structure of the rpgr rcc1-like domain in complex with the2 rpgr-interacting domain of rpgrip1
66c4dmbA_
not modelled 9.2 13
PDB header:immune system
Chain: A: PDB Molecule:hd domain-containing protein 2;
PDBTitle: x-ray structure of human hepatitus c virus ns5a-transactivated protein2 2 at the resolution 1.9a, northeast structural genomics consortium3 (nesg) target hr6723
67c2dnwA_
not modelled 9.0 17
PDB header:transport protein
Chain: A: PDB Molecule:acyl carrier protein;
PDBTitle: solution structure of rsgi ruh-059, an acp domain of acyl2 carrier protein, mitochondrial [precursor] from human cdna
68c2mw4D_
not modelled 8.9 24
PDB header:transcription
Chain: D: PDB Molecule:transcription factor protein;
PDBTitle: tetramerization domain of the ciona intestinalis p53/p73-b2 transcription factor protein
69d2gskb1
not modelled 8.9 17
Fold:TolA/TonB C-terminal domain
Superfamily:TolA/TonB C-terminal domain
Family:TonB
70c3va8A_
not modelled 8.6 5
PDB header:lyase
Chain: A: PDB Molecule:probable dehydratase;
PDBTitle: crystal structure of enolase fg03645.1 (target efi-502278) from2 gibberella zeae ph-1 complexed with magnesium, formate and sulfate
71c2m1mA_
not modelled 8.6 14
PDB header:transcription
Chain: A: PDB Molecule:auxin-induced protein iaa4;
PDBTitle: solution structure of the psiaa4 oligomerization domain reveals2 interaction modes for transcription factors in early auxin response
72c2l9fA_
not modelled 8.5 3
PDB header:transferase
Chain: A: PDB Molecule:cale8;
PDBTitle: nmr solution structure of meacp
73c2p4vA_
not modelled 8.4 12
PDB header:transcription
Chain: A: PDB Molecule:transcription elongation factor greb;
PDBTitle: crystal structure of the transcript cleavage factor, greb2 at 2.6a resolution
74d1ik0a_
not modelled 8.4 14
Fold:4-helical cytokines
Superfamily:4-helical cytokines
Family:Short-chain cytokines
75c5ij6A_
not modelled 8.1 11
PDB header:ligase,transferase
Chain: A: PDB Molecule:lipoate--protein ligase;
PDBTitle: crystal structure of enterococcus faecalis lipoate-protein ligase a2 (lpla-1) in complex with lipoic acid
76c2oqkA_
not modelled 8.0 19
PDB header:translation
Chain: A: PDB Molecule:putative translation initiation factor eif-1a;
PDBTitle: crystal structure of putative cryptosporidium parvum translation2 initiation factor eif-1a
77c5fayA_
not modelled 7.9 19
PDB header:lyase
Chain: A: PDB Molecule:choline trimethylamine-lyase;
PDBTitle: y208f mutant of choline tma-lyase
78c4byl5_
not modelled 7.9 5
PDB header:ribosome
Chain: 5: PDB Molecule:ubiquitin-40s ribosomal protein s31;
PDBTitle: cryo-em reconstruction of the 80s-eif5b-met-itrnamet2 eukaryotic translation initiation complex
79c4uer9_
not modelled 7.9 5
PDB header:translation
Chain: 9: PDB Molecule:es31;
PDBTitle: 40s-eif1-eif1a-eif3-eif3j translation initiation complex from2 lachancea kluyveri
80c3u5cf_
not modelled 7.9 5
PDB header:ribosome
Chain: F: PDB Molecule:40s ribosomal protein s5;
PDBTitle: the structure of the eukaryotic ribosome at 3.0 a resolution. this2 entry contains proteins of the 40s subunit, ribosome a
81c4byt5_
not modelled 7.9 5
PDB header:ribosome
Chain: 5: PDB Molecule:ubiquitin-40s ribosomal protein s31;
PDBTitle: cryo-em reconstruction of the 80s-eif5b-met-itrnamet2 eukaryotic translation initiation complex
82c5fmtB_
not modelled 7.8 17
PDB header:protein transport
Chain: B: PDB Molecule:flagellar associated protein;
PDBTitle: crift54 ch-domain
83d1o98a1
not modelled 7.7 12
Fold:2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain
Superfamily:2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain
Family:2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain
84c5ikfA_
not modelled 7.6 11
PDB header:transcription
Chain: A: PDB Molecule:chromatin remodeling factor mit1;
PDBTitle: crystal structure of the c-terminal domain of the mit1 nucleosome2 remodeler in complex with clr1
85d2up1a2
not modelled 7.6 21
Fold:Ferredoxin-like
Superfamily:RNA-binding domain, RBD
Family:Canonical RBD
86d1qxha_
not modelled 7.5 14
Fold:Thioredoxin fold
Superfamily:Thioredoxin-like
Family:Glutathione peroxidase-like
87c6eacC_
not modelled 7.5 13
PDB header:transferase
Chain: C: PDB Molecule:selo;
PDBTitle: pseudomonas syringae selo
88c4tr3A_
not modelled 7.3 9
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
89d1rtya_
not modelled 7.3 9
Fold:Ferritin-like
Superfamily:Cobalamin adenosyltransferase-like
Family:Cobalamin adenosyltransferase
90c1xx3A_
not modelled 7.1 12
PDB header:transport protein
Chain: A: PDB Molecule:tonb protein;
PDBTitle: solution structure of escherichia coli tonb-ctd
91d2oeza1
not modelled 6.9 18
Fold:YacF-like
Superfamily:YacF-like
Family:YacF-like
92c1rm6E_
not modelled 6.7 16
PDB header:oxidoreductase
Chain: E: PDB Molecule:4-hydroxybenzoyl-coa reductase beta subunit;
PDBTitle: structure of 4-hydroxybenzoyl-coa reductase from thauera2 aromatica
93c4cuyf_
not modelled 6.7 4
PDB header:ribosome
Chain: F: PDB Molecule:us7;
PDBTitle: kluyveromyces lactis 80s ribosome in complex with crpv-ires
94c4f4fB_
not modelled 6.7 11
PDB header:lyase
Chain: B: PDB Molecule:threonine synthase;
PDBTitle: x-ray crystal structure of plp bound threonine synthase from brucella2 melitensis
95c3j81i_
not modelled 6.7 20
PDB header:ribosome
Chain: I: PDB Molecule:es8;
PDBTitle: cryoem structure of a partial yeast 48s preinitiation complex
96c5djnA_
not modelled 6.7 30
PDB header:transport protein
Chain: A: PDB Molecule:kinesin-like protein;
PDBTitle: crystal structure of the kinesin-3 kif13a nc-cc1 mutant - deletion of2 p390
97c3sc0A_
not modelled 6.5 13
PDB header:oxidoreductase
Chain: A: PDB Molecule:methylmalonic aciduria and homocystinuria type c protein;
PDBTitle: crystal structure of mmachc (1-238), a human b12 processing enzyme,2 complexed with methylcobalamin
98d1rtyb_
not modelled 6.5 10
Fold:Ferritin-like
Superfamily:Cobalamin adenosyltransferase-like
Family:Cobalamin adenosyltransferase
99c5ehbA_
not modelled 6.5 35
PDB header:de novo protein
Chain: A: PDB Molecule:phiosyi;
PDBTitle: a de novo designed hexameric coiled-coil peptide with iodotyrosine

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

Transmembrane helix prediction 

Transmembrane helices have been predicted in your sequence to adopt the topology shown below