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1O8C
Asym. Unit
Info
Asym.Unit (219 KB)
Biol.Unit 1 (107 KB)
Biol.Unit 2 (107 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH
Authors
:
G. Sulzenbacher, V. Roig-Zamboni, F. Pagot, S. Grisel, A. Salamoni, C. Valencia, C. Bignon, R. Vincentelli, M. Tegoni, C. Cambillau
Date
:
26 Nov 02 (Deposition) - 21 May 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,D (1x)
Biol. Unit 2: B,C (1x)
Keywords
:
Structural Genomics, Unknown Function, Possible Nadph-Dependent Quinone Oxidoreductase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
G. Sulzenbacher, V. Roig-Zamboni, F. Pagot, S. Grisel, A. Salomoni, C. Valencia, V. Campanacci, R. Vincentelli, M. Tegoni, H. Eklund, C. Cambillau
Structure Of Escherichia Coli Yhdh, A Putative Quinone Oxidoreductase
Acta Crystallogr. , Sect. D V. 60 1855 2004
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPa)
1b: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPb)
1c: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPc)
1d: NADPH DIHYDRO-NICOTINAMIDE-ADENINE... (NDPd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
NDP
4
Ligand/Ion
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:41 , THR A:126 , THR A:130 , GLY A:154 , SER A:156 , GLY A:157 , GLY A:158 , VAL A:159 , SER A:178 , GLY A:179 , ARG A:180 , ARG A:198 , THR A:218 , CYS A:240 , GLY A:241 , LEU A:242 , ALA A:243 , GLY A:244 , ASP A:266 , SER A:267 , VAL A:268 , ILE A:310 , ASN A:313 , HOH A:2051 , HOH A:2114 , HOH A:2115 , HOH A:2116 , HOH A:2117 , HOH A:2118 , ILE D:256
BINDING SITE FOR RESIDUE NDP A1325
2
AC2
SOFTWARE
TYR B:41 , THR B:126 , THR B:130 , GLY B:154 , SER B:156 , GLY B:157 , GLY B:158 , VAL B:159 , SER B:178 , GLY B:179 , ARG B:180 , ARG B:198 , THR B:218 , CYS B:240 , GLY B:241 , LEU B:242 , ALA B:243 , GLY B:244 , ASP B:266 , SER B:267 , VAL B:268 , ILE B:310 , ASN B:313 , ILE B:315 , HOH B:2071 , HOH B:2072 , HOH B:2073 , HOH B:2074 , HOH B:2075 , ILE C:256
BINDING SITE FOR RESIDUE NDP B1325
3
AC3
SOFTWARE
ILE B:256 , TYR C:41 , THR C:126 , THR C:130 , GLY C:154 , SER C:156 , GLY C:157 , GLY C:158 , VAL C:159 , SER C:178 , GLY C:179 , ARG C:180 , ARG C:198 , THR C:218 , VAL C:219 , CYS C:240 , GLY C:241 , LEU C:242 , ALA C:243 , GLY C:244 , ASP C:266 , SER C:267 , VAL C:268 , ILE C:310 , ASN C:313 , HOH C:2086 , HOH C:2091 , HOH C:2092 , HOH C:2093 , HOH C:2094 , HOH C:2095
BINDING SITE FOR RESIDUE NDP C1325
4
AC4
SOFTWARE
ILE A:256 , TYR D:41 , THR D:126 , THR D:130 , GLY D:154 , SER D:156 , GLY D:157 , GLY D:158 , VAL D:159 , SER D:178 , GLY D:179 , ARG D:180 , ARG D:198 , THR D:218 , VAL D:219 , CYS D:240 , GLY D:241 , LEU D:242 , ALA D:243 , GLY D:244 , ASP D:266 , SER D:267 , VAL D:268 , ILE D:310 , ASN D:313 , ILE D:315 , HOH D:2032 , HOH D:2038 , HOH D:2055 , HOH D:2058 , HOH D:2059 , HOH D:2060
BINDING SITE FOR RESIDUE NDP D1325
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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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.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1o8ca3 (A:1-115,A:293-323)
1b: SCOP_d1o8cb3 (B:1-115,B:293-323)
1c: SCOP_d1o8cc1 (C:2-115,C:293-323)
1d: SCOP_d1o8cd3 (D:1-115,D:293-323)
2a: SCOP_d1o8ca4 (A:116-292)
2b: SCOP_d1o8cb4 (B:116-292)
2c: SCOP_d1o8cc3 (C:116-292)
2d: SCOP_d1o8cd4 (D:116-292)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
GroES-like
(132)
Superfamily
:
GroES-like
(130)
Family
:
Alcohol dehydrogenase-like, N-terminal domain
(114)
Protein domain
:
Hypothetical protein YhdH
(2)
Escherichia coli [TaxId: 562]
(2)
1a
d1o8ca3
A:1-115,A:293-323
1b
d1o8cb3
B:1-115,B:293-323
1c
d1o8cc1
C:2-115,C:293-323
1d
d1o8cd3
D:1-115,D:293-323
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Alcohol dehydrogenase-like, C-terminal domain
(115)
Protein domain
:
Hypothetical protein YhdH
(2)
Escherichia coli [TaxId: 562]
(2)
2a
d1o8ca4
A:116-292
2b
d1o8cb4
B:116-292
2c
d1o8cc3
C:116-292
2d
d1o8cd4
D:116-292
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1o8cA02 (A:125-291)
1b: CATH_1o8cB02 (B:125-291)
1c: CATH_1o8cC02 (C:125-291)
1d: CATH_1o8cD02 (D:125-291)
2a: CATH_1o8cA01 (A:1-124,A:292-324)
2b: CATH_1o8cB01 (B:1-124,B:292-324)
2c: CATH_1o8cD01 (D:1-124,D:292-324)
2d: CATH_1o8cC01 (C:2-124,C:292-324)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Escherichia coli. Organism_taxid: 83333. Strain: k-12.
(2)
1a
1o8cA02
A:125-291
1b
1o8cB02
B:125-291
1c
1o8cC02
C:125-291
1d
1o8cD02
D:125-291
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Quinone Oxidoreductase; Chain A, domain 1
(131)
Homologous Superfamily
:
Medium-chain alcohol dehydrogenases, catalytic domain
(131)
Escherichia coli. Organism_taxid: 83333. Strain: k-12.
(2)
2a
1o8cA01
A:1-124,A:292-324
2b
1o8cB01
B:1-124,B:292-324
2c
1o8cD01
D:1-124,D:292-324
2d
1o8cC01
C:2-124,C:292-324
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Pfam Domains
(0, 0)
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