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2VNJ
Asym. Unit
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Asym.Unit (52 KB)
Biol.Unit 1 (48 KB)
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Title
:
X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H) REDUCTASE FROM RHODOBACTER CAPSULATUS IN COMPLEX WITH NADP. FORM I AT 2. 13 ANGSTROMS RESOLUTION
Authors
:
I. Perez-Dorado, J. A. Hermoso
Date
:
05 Feb 08 (Deposition) - 11 Nov 08 (Release) - 20 Jan 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.13
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Electron Transfer, Rhodobacter Capsulatus, Ferredoxin(Flavodoxin)-Nadp(H) Reductase, Nadp, Flavoproteins, Oxidoreductase
(Keyword Search:
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Reference
:
A. Bortolotti, I. Perez-Dorado, G. Goni, M. Medina, J. A. Hermoso, N. Carrillo, N. Cortez
Coenzyme Binding And Hydride Transfer In Rhodobacter Capsulatus Ferredoxin/Flavodoxin Nadp(H) Oxidoreductase.
Biochim. Biophys. Acta V. 1794 199 2009
(for further references see the
PDB file header
)
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Hetero Components
(3, 3)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2a: HEPTYL 1-THIOHEXOPYRANOSIDE (HTGa)
3a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
HTG
1
Ligand/Ion
HEPTYL 1-THIOHEXOPYRANOSIDE
3
NAP
1
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:64 , ALA A:65 , TYR A:66 , SER A:67 , TYR A:80 , SER A:81 , ILE A:82 , VAL A:84 , GLY A:87 , PRO A:88 , LEU A:89 , THR A:90 , THR A:130 , ALA A:133 , LYS A:265 , ALA A:266 , PHE A:267 , VAL A:268 , GLU A:270 , GLY A:271 , HOH A:2025 , HOH A:2031 , HOH A:2057 , HOH A:2118 , HOH A:2120
BINDING SITE FOR RESIDUE FAD A 273
2
AC2
SOFTWARE
THR A:128 , CYS A:157 , ARG A:158 , THR A:194 , ARG A:195 , ARG A:203 , THR A:205 , PHE A:237 , ASP A:240 , ILE A:272 , HOH A:2093
BINDING SITE FOR RESIDUE NAP A 274
3
AC3
SOFTWARE
ARG A:35 , PRO A:71 , ASP A:74 , ARG A:140 , ALA A:172 , LEU A:173 , ASP A:176 , ILE A:179
BINDING SITE FOR RESIDUE HTG A 275
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2vnja1 (A:16-113)
2a: SCOP_d2vnja2 (A:114-272)
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Protein Domains
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(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Reductase/isomerase/elongation factor common domain
(381)
Superfamily
:
Riboflavin synthase domain-like
(130)
Family
:
automated matches
(37)
Protein domain
:
automated matches
(37)
Rhodobacter capsulatus [TaxId: 1061]
(7)
1a
d2vnja1
A:16-113
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ferredoxin reductase-like, C-terminal NADP-linked domain
(120)
Superfamily
:
Ferredoxin reductase-like, C-terminal NADP-linked domain
(120)
Family
:
automated matches
(36)
Protein domain
:
automated matches
(36)
Rhodobacter capsulatus [TaxId: 1061]
(7)
2a
d2vnja2
A:114-272
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2vnjA02 (A:113-266)
2a: CATH_2vnjA01 (A:20-106)
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)
Organisms
(
)
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)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
(85)
Rhodobacter capsulatus. Organism_taxid: 1061. Strain: 37b4. Variant: dsm938.
(6)
1a
2vnjA02
A:113-266
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Elongation Factor Tu (Ef-tu); domain 3
(323)
Homologous Superfamily
:
Translation factors
(223)
Rhodobacter capsulatus. Organism_taxid: 1061. Strain: 37b4. Variant: dsm938.
(6)
2a
2vnjA01
A:20-106
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_FAD_binding_6_2vnjA01 (A:18-114)
2a: PFAM_NAD_binding_1_2vnjA02 (A:125-243)
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Clan
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FAD_Lum_binding
(30)
Family
:
FAD_binding_6
(24)
Rhodobacter capsulatus (Rhodopseudomonas capsulata)
(3)
1a
FAD_binding_6-2vnjA01
A:18-114
Clan
:
NAD_Ferredoxin
(30)
Family
:
NAD_binding_1
(30)
Rhodobacter capsulatus (Rhodopseudomonas capsulata)
(3)
2a
NAD_binding_1-2vnjA02
A:125-243
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Asymmetric Unit 1
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