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2VNK
Biol. Unit 3
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Asym.Unit (195 KB)
Biol.Unit 1 (51 KB)
Biol.Unit 2 (50 KB)
Biol.Unit 3 (51 KB)
Biol.Unit 4 (50 KB)
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(1)
Title
:
X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H) REDUCTASE FROM RHODOBACTER CAPSULATUS IN COMPLEX WITH NADP. FORM III AT 1. 93 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
:
1.93
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Electron Transfer, Rhodobacter Capsulatus, Ferredoxin(Flavodoxin)-Nadp(H) Reductase, Nadp, Flavoproteins, Oxidoreductase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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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
(2, 2)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
1c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
1d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
2a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
2b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
2c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
2d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
NAP
1
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
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Sites
(2, 2)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
ARG C:64 , ALA C:65 , TYR C:66 , SER C:67 , TYR C:80 , SER C:81 , ILE C:82 , VAL C:84 , GLY C:87 , PRO C:88 , LEU C:89 , THR C:90 , THR C:130 , ALA C:133 , LYS C:265 , ALA C:266 , PHE C:267 , VAL C:268 , GLY C:269 , GLU C:270 , GLY C:271 , ILE C:272 , HOH C:2060 , HOH C:2061 , HOH C:2226 , HOH C:2227 , HOH C:2228 , HOH C:2229 , HOH C:2230 , HOH C:2231 , HOH C:2232
BINDING SITE FOR RESIDUE FAD C 273
2
AC6
SOFTWARE
THR C:128 , CYS C:157 , ARG C:158 , THR C:194 , ARG C:195 , ARG C:203 , THR C:205 , ALA C:236 , PHE C:237 , ASP C:240 , ILE C:272 , HOH C:2139 , HOH C:2175 , HOH C:2233 , HOH C:2234 , HOH C:2235 , HOH C:2236
BINDING SITE FOR RESIDUE NAP C 274
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2vnka1 (A:16-113)
1b: SCOP_d2vnkb1 (B:16-113)
1c: SCOP_d2vnkc1 (C:16-113)
1d: SCOP_d2vnkd1 (D:16-113)
2a: SCOP_d2vnka2 (A:114-272)
2b: SCOP_d2vnkb2 (B:114-269)
2c: SCOP_d2vnkc2 (C:114-272)
2d: SCOP_d2vnkd2 (D:114-269)
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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
d2vnka1
A:16-113
1b
d2vnkb1
B:16-113
1c
d2vnkc1
C:16-113
1d
d2vnkd1
D: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
d2vnka2
A:114-272
2b
d2vnkb2
B:114-269
2c
d2vnkc2
C:114-272
2d
d2vnkd2
D:114-269
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2vnkA02 (A:113-266)
1b: CATH_2vnkB02 (B:113-266)
1c: CATH_2vnkC02 (C:113-266)
1d: CATH_2vnkD02 (D:113-266)
2a: CATH_2vnkA01 (A:20-106)
2b: CATH_2vnkB01 (B:20-106)
2c: CATH_2vnkC01 (C:20-106)
2d: CATH_2vnkD01 (D:20-106)
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)
Organisms
(
)
(
)
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
2vnkA02
A:113-266
1b
2vnkB02
B:113-266
1c
2vnkC02
C:113-266
1d
2vnkD02
D: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
2vnkA01
A:20-106
2b
2vnkB01
B:20-106
2c
2vnkC01
C:20-106
2d
2vnkD01
D:20-106
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_FAD_binding_6_2vnkD01 (D:18-114)
1b: PFAM_FAD_binding_6_2vnkD02 (D:18-114)
1c: PFAM_FAD_binding_6_2vnkD03 (D:18-114)
1d: PFAM_FAD_binding_6_2vnkD04 (D:18-114)
2a: PFAM_NAD_binding_1_2vnkD05 (D:125-243)
2b: PFAM_NAD_binding_1_2vnkD06 (D:125-243)
2c: PFAM_NAD_binding_1_2vnkD07 (D:125-243)
2d: PFAM_NAD_binding_1_2vnkD08 (D:125-243)
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Clan
:
FAD_Lum_binding
(30)
Family
:
FAD_binding_6
(24)
Rhodobacter capsulatus (Rhodopseudomonas capsulata)
(3)
1a
FAD_binding_6-2vnkD01
D:18-114
1b
FAD_binding_6-2vnkD02
D:18-114
1c
FAD_binding_6-2vnkD03
D:18-114
1d
FAD_binding_6-2vnkD04
D:18-114
Clan
:
NAD_Ferredoxin
(30)
Family
:
NAD_binding_1
(30)
Rhodobacter capsulatus (Rhodopseudomonas capsulata)
(3)
2a
NAD_binding_1-2vnkD05
D:125-243
2b
NAD_binding_1-2vnkD06
D:125-243
2c
NAD_binding_1-2vnkD07
D:125-243
2d
NAD_binding_1-2vnkD08
D:125-243
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Chain C
Asymmetric Unit 1
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Asym.Unit (195 KB)
Header - Asym.Unit
Biol.Unit 1 (51 KB)
Header - Biol.Unit 1
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Biol.Unit 3 (51 KB)
Header - Biol.Unit 3
Biol.Unit 4 (50 KB)
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