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2QFV
Biol. Unit 1
Info
Asym.Unit (289 KB)
Biol.Unit 1 (144 KB)
Biol.Unit 2 (143 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVESIAE MITOCHONDRIAL NADP(+)-DEPENDENT ISOCITRATE DEHYDROGENASE IN COMPLEX WITH NADP(+)
Authors
:
Y. J. Peng, J. P. Ding
Date
:
28 Jun 07 (Deposition) - 01 Jul 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Rossmann Fold, Oxidoreductase
(Keyword Search:
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Reference
:
Y. J. Peng, C. Zhong, W. Huang, J. P. Ding
Structural Studies Of Saccharomyces Cerevesiae Mitochondrial Nadp-Dependent Isocitrate Dehydrogenase In Different Enzymatic States Reveal Substantial Conformational Changes During The Catalytic Reaction
Protein Sci. V. 17 1542 2008
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
1b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
1c: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPc)
1d: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPd)
View:
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No.
Name
Count
Type
Full Name
1
NAP
2
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:73 , ALA A:75 , THR A:76 , ILE A:77 , THR A:78 , ARG A:83 , ASN A:97 , GLU A:308 , HIS A:311 , GLY A:312 , THR A:313 , THR A:315 , ARG A:316 , HIS A:317 , ASN A:330 , HOH A:1007 , HOH A:1061 , HOH A:1075 , HOH A:1145 , HOH A:1204 , GLN D:59
BINDING SITE FOR RESIDUE NAP A 1001
2
AC2
SOFTWARE
LYS B:73 , ALA B:75 , THR B:76 , ILE B:77 , THR B:78 , ASN B:97 , GLU B:308 , HIS B:311 , GLY B:312 , THR B:313 , ARG B:316 , HIS B:317 , ASN B:330 , HOH B:1014 , HOH B:1067 , HOH B:1181
BINDING SITE FOR RESIDUE NAP B 1002
3
AC4
SOFTWARE
GLN A:59 , LYS D:73 , ALA D:75 , THR D:76 , ILE D:77 , THR D:78 , ARG D:83 , ASN D:97 , GLU D:308 , HIS D:311 , GLY D:312 , THR D:313 , THR D:315 , ARG D:316 , HIS D:317 , THR D:329 , ASN D:330 , HOH D:1029 , HOH D:1030 , HOH D:1080 , HOH D:1161
BINDING SITE FOR RESIDUE NAP D 1004
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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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: IDH_IMDH (A:273-292,B:273-292)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IDH_IMDH
PS00470
Isocitrate and isopropylmalate dehydrogenases signature.
IDHP_YEAST
288-307
2
A:273-292
B:273-292
-
-
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Exons
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SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2qfva_ (A:)
1b: SCOP_d2qfvb_ (B:)
1c: SCOP_d2qfvc_ (C:)
1d: SCOP_d2qfvd_ (D:)
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Protein Domains
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Organisms
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Isocitrate/Isopropylmalate dehydrogenase-like
(143)
Superfamily
:
Isocitrate/Isopropylmalate dehydrogenase-like
(143)
Family
:
Dimeric isocitrate & isopropylmalate dehydrogenases
(102)
Protein domain
:
automated matches
(45)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(4)
1a
d2qfva_
A:
1b
d2qfvb_
B:
1c
d2qfvc_
C:
1d
d2qfvd_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2qfvB00 (B:4-411)
1b: CATH_2qfvC00 (C:3-410)
1c: CATH_2qfvA00 (A:2-411)
1d: CATH_2qfvD00 (D:2-411)
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Organisms
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)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Isopropylmalate Dehydrogenase
(91)
Homologous Superfamily
:
Isopropylmalate Dehydrogenase
(91)
Yeast (Saccharomyces cerevisiae)
(4)
1a
2qfvB00
B:4-411
1b
2qfvC00
C:3-410
1c
2qfvA00
A:2-411
1d
2qfvD00
D:2-411
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Iso_dh_2qfvD01 (D:6-401)
1b: PFAM_Iso_dh_2qfvD02 (D:6-401)
1c: PFAM_Iso_dh_2qfvD03 (D:6-401)
1d: PFAM_Iso_dh_2qfvD04 (D:6-401)
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Clan
:
Iso_DH
(49)
Family
:
Iso_dh
(38)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(3)
1a
Iso_dh-2qfvD01
D:6-401
1b
Iso_dh-2qfvD02
D:6-401
1c
Iso_dh-2qfvD03
D:6-401
1d
Iso_dh-2qfvD04
D:6-401
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (289 KB)
Header - Asym.Unit
Biol.Unit 1 (144 KB)
Header - Biol.Unit 1
Biol.Unit 2 (143 KB)
Header - Biol.Unit 2
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