Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD2255A_(RVBD2255A)_2529104_2529322
DateMon Aug 5 13:25:39 BST 2019
Unique Job ID389d1af49b1299b6
SequenceVRLRPAEDSD ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:23.140 Y:34.269 Z:41.174
Model (left) based on template d2cg4a2
Top template information
Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:Lrp/AsnC-like transcriptional regulator C-terminal domain
Confidence and coverage
Confidence: 99.7% Coverage:100%
72 residues (100% of your sequence) have been modelled with 99.7% 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
1d2cg4a2



99.7 24
Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:Lrp/AsnC-like transcriptional regulator C-terminal domain
2d2cyya2



99.7 20
Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:Lrp/AsnC-like transcriptional regulator C-terminal domain
3d1i1ga2



99.7 12
Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:Lrp/AsnC-like transcriptional regulator C-terminal domain
4c2djwF_



99.7 23
PDB header:unknown function
Chain: F: PDB Molecule:probable transcriptional regulator, asnc family;
PDBTitle: crystal structure of ttha0845 from thermus thermophilus hb8
5d2cfxa2



99.7 19
Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:Lrp/AsnC-like transcriptional regulator C-terminal domain
6c2zbcH_



99.7 13
PDB header:transcription
Chain: H: PDB Molecule:83aa long hypothetical transcriptional regulator asnc;
PDBTitle: crystal structure of sts042, a stand-alone ram module protein, from2 hyperthermophilic archaeon sulfolobus tokodaii strain7.
7c2e1aD_



99.6 19
PDB header:transcription
Chain: D: PDB Molecule:75aa long hypothetical regulatory protein asnc;
PDBTitle: crystal structure of ffrp-dm1
8c2cg4B_



99.5 24
PDB header:transcription
Chain: B: PDB Molecule:regulatory protein asnc;
PDBTitle: structure of e.coli asnc
9c1i1gA_



99.5 12
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator lrpa;
PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus
10c3i4pA_



99.5 21
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, asnc family;
PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens
11c4pcqC_



99.5 24
PDB header:transcription
Chain: C: PDB Molecule:possible transcriptional regulatory protein (probably
PDBTitle: crystal structure of mtbaldr (rv2779c)
12c2e1cA_



99.5 21
PDB header:transcription/dna
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph1519;
PDBTitle: structure of putative hth-type transcriptional regulator ph1519/dna2 complex
13c2e7xA_



99.5 13
PDB header:transcription regulator
Chain: A: PDB Molecule:150aa long hypothetical transcriptional regulator;
PDBTitle: structure of the lrp/asnc like transcriptional regulator from2 sulfolobus tokodaii 7 complexed with its cognate ligand
14c2gqqB_



99.5 24
PDB header:transcription
Chain: B: PDB Molecule:leucine-responsive regulatory protein;
PDBTitle: crystal structure of e. coli leucine-responsive regulatory protein2 (lrp)
15c2p6tH_



99.4 21
PDB header:transcription
Chain: H: PDB Molecule:transcriptional regulator, lrp/asnc family;
PDBTitle: crystal structure of transcriptional regulator nmb0573 and l-leucine2 complex from neisseria meningitidis
16c2cfxD_



99.4 20
PDB header:transcription
Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc;
PDBTitle: structure of b.subtilis lrpc
17c2dbbA_



99.4 16
PDB header:transcriptional regulator
Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061;
PDBTitle: crystal structure of ph0061
18c2vbzA_



99.4 25
PDB header:dna-binding protein
Chain: A: PDB Molecule:transcriptional regulatory protein;
PDBTitle: feast or famine regulatory protein (rv3291c)from m.2 tuberculosis complexed with l-tryptophan
19c2ia0A_



99.3 6
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative hth-type transcriptional regulator pf0864;
PDBTitle: transcriptional regulatory protein pf0864 from pyrococcus furiosus a2 member of the asnc family (pf0864)
20c4ch7A_



99.2 6
PDB header:transcription
Chain: A: PDB Molecule:nird-like protein;
PDBTitle: crystal structure of the siroheme decarboxylase nirdl
21c4czdD_



not modelled 99.2 13
PDB header:lyase
Chain: D: PDB Molecule:putative transcriptional regulator, asnc family;
PDBTitle: sirohaem decarboxylase ahba/b - an enzyme with structural homology2 to the lrp/asnc transcription factor family that is part of the3 alternative haem biosynthesis pathway.
22c4czdA_



not modelled 99.1 10
PDB header:lyase
Chain: A: PDB Molecule:putative transcriptional regulator, asnc family;
PDBTitle: sirohaem decarboxylase ahba/b - an enzyme with structural homology2 to the lrp/asnc transcription factor family that is part of the3 alternative haem biosynthesis pathway.
23c2jsxA_



not modelled 94.3 11
PDB header:chaperone
Chain: A: PDB Molecule:protein napd;
PDBTitle: solution structure of the e. coli tat proofreading2 chaperone protein napd
24c3ibwA_



not modelled 89.3 24
PDB header:transferase
Chain: A: PDB Molecule:gtp pyrophosphokinase;
PDBTitle: crystal structure of the act domain from gtp pyrophosphokinase of2 chlorobium tepidum. northeast structural genomics consortium target3 ctr148a
25c4qo6A_



not modelled 78.3 13
PDB header:structural protein
Chain: A: PDB Molecule:adenylate cyclase-like protein;
PDBTitle: structural studies of cdsd, a structural protein of the type iii2 secretion system (ttss) of chlamydia trachomatis
26c4n8oA_



not modelled 76.2 7
PDB header:membrane protein
Chain: A: PDB Molecule:cell division protein ftsx;
PDBTitle: crystal structure of mycobacterial ftsx extracellular domain, bromide2 derivative
27c6mk7A_



not modelled 71.0 11
PDB header:membrane protein
Chain: A: PDB Molecule:cell division protein ftsx;
PDBTitle: solution structure of the large extracellular loop of ftsx in2 streptococcus pneumoniae
28c3bn7A_



not modelled 65.6 20
PDB header:unknown function
Chain: A: PDB Molecule:ferredoxin-like protein;
PDBTitle: crystal structure of a dimeric ferredoxin-like protein (cc_2267) from2 caulobacter crescentus cb15 at 1.64 a resolution
29c2a5hC_



not modelled 64.8 17
PDB header:isomerase
Chain: C: PDB Molecule:l-lysine 2,3-aminomutase;
PDBTitle: 2.1 angstrom x-ray crystal structure of lysine-2,3-aminomutase from2 clostridium subterminale sb4, with michaelis analog (l-alpha-lysine3 external aldimine form of pyridoxal-5'-phosphate).
30d1j5ya2



not modelled 57.2 18
Fold:HPr-like
Superfamily:Putative transcriptional regulator TM1602, C-terminal domain
Family:Putative transcriptional regulator TM1602, C-terminal domain
31d1q5ya_



not modelled 51.9 7
Fold:Ferredoxin-like
Superfamily:ACT-like
Family:Nickel responsive regulator NikR, C-terminal domain
32c1q5vB_



not modelled 50.5 7
PDB header:transcription
Chain: B: PDB Molecule:nickel responsive regulator;
PDBTitle: apo-nikr
33c2y3yC_



not modelled 42.7 11
PDB header:transcription
Chain: C: PDB Molecule:putative nickel-responsive regulator;
PDBTitle: holo-ni(ii) hpnikr is a symmetric tetramer containing four canonic2 square-planar ni(ii) ions at physiological ph
34c3bdeA_



not modelled 41.6 13
PDB header:unknown function
Chain: A: PDB Molecule:mll5499 protein;
PDBTitle: crystal structure of a dabb family protein with a ferredoxin-like fold2 (mll5499) from mesorhizobium loti maff303099 at 1.79 a resolution
35d1mlia_



not modelled 41.4 17
Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:Muconalactone isomerase, MLI
36d1uj4a2



not modelled 39.7 19
Fold:Ferredoxin-like
Superfamily:D-ribose-5-phosphate isomerase (RpiA), lid domain
Family:D-ribose-5-phosphate isomerase (RpiA), lid domain
37d1o8ba2



not modelled 39.6 11
Fold:Ferredoxin-like
Superfamily:D-ribose-5-phosphate isomerase (RpiA), lid domain
Family:D-ribose-5-phosphate isomerase (RpiA), lid domain
38d1lk5a2



not modelled 39.1 11
Fold:Ferredoxin-like
Superfamily:D-ribose-5-phosphate isomerase (RpiA), lid domain
Family:D-ribose-5-phosphate isomerase (RpiA), lid domain
39c3znuI_



not modelled 38.4 16
PDB header:lyase
Chain: I: PDB Molecule:5-chloromuconolactone dehalogenase;
PDBTitle: crystal structure of clcf in crystal form 2
40c4wwsE_



not modelled 38.2 10
PDB header:oxidoreductase
Chain: E: PDB Molecule:putative heme-dependent peroxidase lmo2113;
PDBTitle: structure of chlorite dismutase-like protein from listeria2 monocytogenes
41d1m0sa2



not modelled 37.8 14
Fold:Ferredoxin-like
Superfamily:D-ribose-5-phosphate isomerase (RpiA), lid domain
Family:D-ribose-5-phosphate isomerase (RpiA), lid domain
42c5a13J_



not modelled 36.4 20
PDB header:oxidoreductase
Chain: J: PDB Molecule:chlorite dismutase;
PDBTitle: crystal structure of chlorite dismutase from2 magnetospirillum sp. in complex with thiocyanate
43c2ca9B_



not modelled 30.9 12
PDB header:transcription
Chain: B: PDB Molecule:putative nickel-responsive regulator;
PDBTitle: apo-nikr from helicobacter pylori in closed trans-2 conformation
44d1rwua_



not modelled 29.2 16
Fold:Ferredoxin-like
Superfamily:YbeD/HP0495-like
Family:YbeD-like
45c1rwuA_



not modelled 29.2 16
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical upf0250 protein ybed;
PDBTitle: solution structure of conserved protein ybed from e. coli
46d2joqa1



not modelled 28.3 6
Fold:Ferredoxin-like
Superfamily:YbeD/HP0495-like
Family:HP0495-like
47c2bj3D_



not modelled 27.7 5
PDB header:transcription
Chain: D: PDB Molecule:nickel responsive regulator;
PDBTitle: nikr-apo
48c3nn4C_



not modelled 26.3 8
PDB header:oxidoreductase
Chain: C: PDB Molecule:chlorite dismutase;
PDBTitle: structure of chlorite dismutase from candidatus nitrospira defluvii2 r173k mutant
49c1lk5C_



not modelled 25.5 11
PDB header:isomerase
Chain: C: PDB Molecule:d-ribose-5-phosphate isomerase;
PDBTitle: structure of the d-ribose-5-phosphate isomerase from2 pyrococcus horikoshii
50c3l7oB_



not modelled 24.9 11
PDB header:isomerase
Chain: B: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-phosphate isomerase a from streptococcus2 mutans ua159
51c3kwmC_



not modelled 23.9 11
PDB header:isomerase
Chain: C: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-isomerase a
52c6j1kA_



not modelled 23.6 17
PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-phosphate isomerase a from ochrobactrum2 sp. csl1
53c4gmkB_



not modelled 21.8 11
PDB header:isomerase
Chain: B: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose 5-phosphate isomerase from the probiotic2 bacterium lactobacillus salivarius ucc118
54c4x84C_



not modelled 21.7 8
PDB header:isomerase
Chain: C: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-phosphate isomerase a from pseudomonas2 aeruginosa
55c1uj6A_



not modelled 21.6 19
PDB header:isomerase
Chain: A: PDB Molecule:ribose 5-phosphate isomerase;
PDBTitle: crystal structure of thermus thermophilus ribose-5-phosphate isomerase2 complexed with arabinose-5-phosphate
56c2vxhF_



not modelled 21.4 19
PDB header:oxidoreductase
Chain: F: PDB Molecule:chlorite dismutase;
PDBTitle: the crystal structure of chlorite dismutase: a detox enzyme2 producing molecular oxygen
57c1lkzB_



not modelled 21.0 11
PDB header:isomerase
Chain: B: PDB Molecule:ribose 5-phosphate isomerase a;
PDBTitle: crystal structure of d-ribose-5-phosphate isomerase (rpia) from2 escherichia coli.
58c3u7jA_



not modelled 20.3 14
PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-phosphate isomerase a from burkholderia2 thailandensis
59c5y02D_



not modelled 20.1 9
PDB header:lyase
Chain: D: PDB Molecule:hydroxynitrile lyase;
PDBTitle: c-terminal peptide depleted mutant of hydroxynitrile lyase from2 passiflora edulis (pehnl) bound with (r)-mandelonitrile
60c6eepA_



not modelled 19.3 14
PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-phosphate isomerase from legionella2 pneumophila
61c1m0sA_



not modelled 19.1 14
PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: northeast structural genomics consortium (nesg id ir21)
62c1xtzA_



not modelled 19.1 19
PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase;
PDBTitle: crystal structure of the s. cerevisiae d-ribose-5-phosphate isomerase:2 comparison with the archeal and bacterial enzymes
63c2f8mB_



not modelled 18.6 16
PDB header:isomerase
Chain: B: PDB Molecule:ribose 5-phosphate isomerase;
PDBTitle: ribose 5-phosphate isomerase from plasmodium falciparum
64c5uf2A_



not modelled 18.6 3
PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose 5 phosphate isomerase a from neisseria2 gonorrhoeae
65c3hheA_



not modelled 17.4 8
PDB header:isomerase
Chain: A: PDB Molecule:ribose-5-phosphate isomerase a;
PDBTitle: crystal structure of ribose-5-phosphate isomerase a from bartonella2 henselae
66c3sf5D_



not modelled 17.4 11
PDB header:chaperone
Chain: D: PDB Molecule:urease accessory protein ureh;
PDBTitle: crystal structure of helicobacter pylori urease accessory protein2 uref/h complex
67d1uw4a_



not modelled 16.8 13
Fold:Ferredoxin-like
Superfamily:RNA-binding domain, RBD
Family:Smg-4/UPF3
68c3qpiA_



not modelled 16.3 17
PDB header:oxidoreductase
Chain: A: PDB Molecule:chlorite dismutase;
PDBTitle: crystal structure of dimeric chlorite dismutases from nitrobacter2 winogradskyi
69c3bguA_



not modelled 16.2 9
PDB header:unknown function
Chain: A: PDB Molecule:ferredoxin-like protein of unknown function;
PDBTitle: crystal structure of a dimeric ferredoxin-like protein of unknown2 function (tfu_0763) from thermobifida fusca yx at 1.50 a resolution
70d1sc6a3



not modelled 15.7 11
Fold:Ferredoxin-like
Superfamily:ACT-like
Family:Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
71d2nzca1



not modelled 15.6 11
Fold:Ferredoxin-like
Superfamily:ACT-like
Family:TM1266-like
72d1rjja_



not modelled 15.1 8
Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:Plant stress-induced protein
73d2bj7a2



not modelled 14.9 5
Fold:Ferredoxin-like
Superfamily:ACT-like
Family:Nickel responsive regulator NikR, C-terminal domain
74d1vdha_



not modelled 14.0 17
Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:Chlorite dismutase-like
75c5z2vB_



not modelled 13.6 17
PDB header:dna binding protein
Chain: B: PDB Molecule:recombination protein recr;
PDBTitle: crystal structure of recr from pseudomonas aeruginosa pao1
76d1t0tv_



not modelled 12.9 17
Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:Chlorite dismutase-like
77c5zvqA_



not modelled 12.2 19
PDB header:recombination
Chain: A: PDB Molecule:recombination protein recr;
PDBTitle: crystal structure of recombination mediator protein recr
78d1vdda_



not modelled 12.1 19
Fold:Recombination protein RecR
Superfamily:Recombination protein RecR
Family:Recombination protein RecR
79c1vddC_



not modelled 11.1 22
PDB header:recombination
Chain: C: PDB Molecule:recombination protein recr;
PDBTitle: crystal structure of recombinational repair protein recr
80c2yadA_



not modelled 11.1 21
PDB header:surfactant protein
Chain: A: PDB Molecule:surfactant protein c brichos domain;
PDBTitle: brichos domain of surfactant protein c precursor protein
81c4nmlA_



not modelled 11.1 22
PDB header:isomerase
Chain: A: PDB Molecule:ribulose 5-phosphate isomerase;
PDBTitle: 2.60 angstrom resolution crystal structure of putative ribose 5-2 phosphate isomerase from toxoplasma gondii me49 in complex with dl-3 malic acid
82c5yaaD_



not modelled 10.8 17
PDB header:hydrolase
Chain: D: PDB Molecule:meiosis regulator and mrna stability factor 1;
PDBTitle: crystal structure of marf1 nyn domain from mus musculus
83c5k8zB_



not modelled 10.7 16
PDB header:oxidoreductase
Chain: B: PDB Molecule:chlorite dismutase;
PDBTitle: crystal structure of dimeric chlorite dismutase from cyanothece sp.2 pcc7425 (ph 8.5)
84c2pbeA_



not modelled 10.4 25
PDB header:transferase
Chain: A: PDB Molecule:aminoglycoside 6-adenylyltransferase;
PDBTitle: crystal structure of an aminoglycoside 6-adenyltransferase2 from bacillus subtilis
85d1pv8a_



not modelled 9.9 18
Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)
86c3dtzB_



not modelled 9.4 15
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative chlorite dismutase ta0507;
PDBTitle: crystal structure of putative chlorite dismutase ta0507
87c2yadE_



not modelled 9.1 26
PDB header:surfactant protein
Chain: E: PDB Molecule:surfactant protein c brichos domain;
PDBTitle: brichos domain of surfactant protein c precursor protein
88c5nocA_



not modelled 8.9 35
PDB header:dna binding protein
Chain: A: PDB Molecule:stage 0 sporulation protein j;
PDBTitle: solution nmr structure of the c-terminal domain of parb (spo0j)
89c5lzlH_



not modelled 8.6 23
PDB header:lyase
Chain: H: PDB Molecule:delta-aminolevulinic acid dehydratase;
PDBTitle: pyrobaculum calidifontis 5-aminolaevulinic acid dehydratase
90c3bb5B_



not modelled 8.4 17
PDB header:unknown function
Chain: B: PDB Molecule:stress responsive alpha-beta protein;
PDBTitle: crystal structure of a dimeric ferredoxin-like protein of unknown2 function (jann_3925) from jannaschia sp. ccs1 at 2.30 a resolution
91d2pbea2



not modelled 8.0 26
Fold:Nucleotidyltransferase
Superfamily:Nucleotidyltransferase
Family:AadK N-terminal domain-like
92c3iplB_



not modelled 7.8 16
PDB header:ligase
Chain: B: PDB Molecule:2-succinylbenzoate--coa ligase;
PDBTitle: crystal structure of o-succinylbenzoic acid-coa ligase from2 staphylococcus aureus subsp. aureus mu50
93c3zmnA_



not modelled 7.2 20
PDB header:viral protein
Chain: A: PDB Molecule:vp17;
PDBTitle: vp17, a capsid protein of bacteriophage p23-77
94d2icya1



not modelled 7.2 17
Fold:Single-stranded left-handed beta-helix
Superfamily:Trimeric LpxA-like enzymes
Family:GlmU C-terminal domain-like
95c2lqjA_



not modelled 7.1 21
PDB header:hydrolase
Chain: A: PDB Molecule:mg2+ transport protein;
PDBTitle: solution structure of the c-terminal domain of the mgtc protein from2 mycobacterium tuberculosis
96c2l2eA_



not modelled 6.9 29
PDB header:metal binding protein
Chain: A: PDB Molecule:calcium-binding protein ncs-1;
PDBTitle: solution nmr structure of myristoylated ncs1p in apo form
97d1f0la3



not modelled 6.3 17
Fold:Toxins' membrane translocation domains
Superfamily:Diphtheria toxin, middle domain
Family:Diphtheria toxin, middle domain
98c3g7sA_



not modelled 6.1 21
PDB header:ligase
Chain: A: PDB Molecule:long-chain-fatty-acid--coa ligase (fadd-1);
PDBTitle: crystal structure of a long-chain-fatty-acid-coa ligase2 (fadd1) from archaeoglobus fulgidus
99d1q4ra_



not modelled 5.9 6
Fold:Ferredoxin-like
Superfamily:Dimeric alpha+beta barrel
Family:Plant stress-induced protein

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