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1YKF
Asym. Unit
Info
Asym.Unit (226 KB)
Biol.Unit 1 (220 KB)
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(1)
Title
:
NADP-DEPENDENT ALCOHOL DEHYDROGENASE FROM THERMOANAEROBIUM BROCKII
Authors
:
Y. Korkhin, F. Frolow
Date
:
25 Mar 96 (Deposition) - 14 Jan 98 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Korkhin, A. J. Kalb(Gilboa), M. Peretz, O. Bogin, Y. Burstein, F. Frolow
Nadp-Dependent Bacterial Alcohol Dehydrogenases: Crystal Structure, Cofactor-Binding And Cofactor Specificity Of The Adhs Of Clostridium Beijerinckii And Thermoanaerobacter Brockii.
J. Mol. Biol. V. 278 967 1998
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 8)
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)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAP
4
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2
ZN
4
Ligand/Ion
ZINC ION
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:37 , SER A:39 , HIS A:59 , ASP A:150
BINDING SITE FOR RESIDUE ZN A 354
2
AC2
SOFTWARE
CYS B:37 , HIS B:59 , ASP B:150 , NAP B:353
BINDING SITE FOR RESIDUE ZN B 354
3
AC3
SOFTWARE
CYS C:37 , SER C:39 , HIS C:59 , ASP C:150 , NAP C:353
BINDING SITE FOR RESIDUE ZN C 354
4
AC4
SOFTWARE
CYS D:37 , SER D:39 , HIS D:59 , ASP D:150 , NAP D:353
BINDING SITE FOR RESIDUE ZN D 354
5
AC5
SOFTWARE
THR A:38 , SER A:39 , HIS A:42 , ASP A:150 , THR A:154 , GLY A:174 , ILE A:175 , GLY A:176 , PRO A:177 , VAL A:178 , SER A:199 , ARG A:200 , TYR A:218 , ALA A:242 , VAL A:265 , ASN A:266 , TYR A:267
BINDING SITE FOR RESIDUE NAP A 353
6
AC6
SOFTWARE
THR B:38 , SER B:39 , HIS B:42 , ASP B:150 , THR B:154 , GLY B:174 , ILE B:175 , GLY B:176 , PRO B:177 , VAL B:178 , SER B:199 , ARG B:200 , TYR B:218 , ALA B:242 , VAL B:265 , ASN B:266 , TYR B:267 , ZN B:354
BINDING SITE FOR RESIDUE NAP B 353
7
AC7
SOFTWARE
THR C:38 , SER C:39 , HIS C:42 , ASP C:150 , THR C:154 , GLY C:174 , ILE C:175 , GLY C:176 , PRO C:177 , VAL C:178 , SER C:199 , ARG C:200 , TYR C:218 , ILE C:223 , ALA C:242 , VAL C:265 , ASN C:266 , TYR C:267 , ZN C:354
BINDING SITE FOR RESIDUE NAP C 353
8
AC8
SOFTWARE
SER D:39 , HIS D:42 , ASP D:150 , THR D:154 , GLY D:174 , ILE D:175 , GLY D:176 , PRO D:177 , VAL D:178 , SER D:199 , ARG D:200 , TYR D:218 , ILE D:223 , ALA D:242 , VAL D:265 , ASN D:266 , TYR D:267 , ZN D:354
BINDING SITE FOR RESIDUE NAP D 353
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ADH_ZINC (A:58-72,B:58-72,C:58-72,D:58-72)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADH_ZINC
PS00059
Zinc-containing alcohol dehydrogenases signature.
ADH_THEBR
58-72
4
A:58-72
B:58-72
C:58-72
D:58-72
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Exons
(0, 0)
Info
All Exons
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Note:
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_d1ykfa1 (A:1-139,A:314-352)
1b: SCOP_d1ykfb1 (B:1-139,B:314-352)
1c: SCOP_d1ykfc1 (C:1-139,C:314-352)
1d: SCOP_d1ykfd1 (D:1-139,D:314-352)
2a: SCOP_d1ykfa2 (A:140-313)
2b: SCOP_d1ykfb2 (B:140-313)
2c: SCOP_d1ykfc2 (C:140-313)
2d: SCOP_d1ykfd2 (D:140-313)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
GroES-like
(132)
Superfamily
:
GroES-like
(130)
Family
:
Alcohol dehydrogenase-like, N-terminal domain
(114)
Protein domain
:
Bacterial secondary alcohol dehydrogenase
(7)
Thermoanaerobacter brockii [TaxId: 29323]
(3)
1a
d1ykfa1
A:1-139,A:314-352
1b
d1ykfb1
B:1-139,B:314-352
1c
d1ykfc1
C:1-139,C:314-352
1d
d1ykfd1
D:1-139,D:314-352
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
:
Bacterial secondary alcohol dehydrogenase
(7)
Thermoanaerobacter brockii [TaxId: 29323]
(3)
2a
d1ykfa2
A:140-313
2b
d1ykfb2
B:140-313
2c
d1ykfc2
C:140-313
2d
d1ykfd2
D:140-313
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1ykfA02 (A:162-292)
1b: CATH_1ykfB02 (B:162-292)
1c: CATH_1ykfC02 (C:162-292)
1d: CATH_1ykfD02 (D:162-292)
2a: CATH_1ykfA01 (A:1-161,A:293-352)
2b: CATH_1ykfB01 (B:1-161,B:293-352)
2c: CATH_1ykfC01 (C:1-161,C:293-352)
2d: CATH_1ykfD01 (D:1-161,D:293-352)
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)
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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)
Thermoanaerobacter brockii. Organism_taxid: 29323.
(2)
1a
1ykfA02
A:162-292
1b
1ykfB02
B:162-292
1c
1ykfC02
C:162-292
1d
1ykfD02
D:162-292
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Quinone Oxidoreductase; Chain A, domain 1
(131)
Homologous Superfamily
:
Medium-chain alcohol dehydrogenases, catalytic domain
(131)
Thermoanaerobacter brockii. Organism_taxid: 29323.
(2)
2a
1ykfA01
A:1-161,A:293-352
2b
1ykfB01
B:1-161,B:293-352
2c
1ykfC01
C:1-161,C:293-352
2d
1ykfD01
D:1-161,D:293-352
[
close CATH info
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_ADH_N_1ykfD01 (D:24-135)
1b: PFAM_ADH_N_1ykfD02 (D:24-135)
1c: PFAM_ADH_N_1ykfD03 (D:24-135)
1d: PFAM_ADH_N_1ykfD04 (D:24-135)
2a: PFAM_ADH_zinc_N_1ykfD05 (D:177-310)
2b: PFAM_ADH_zinc_N_1ykfD06 (D:177-310)
2c: PFAM_ADH_zinc_N_1ykfD07 (D:177-310)
2d: PFAM_ADH_zinc_N_1ykfD08 (D:177-310)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GroES
(70)
Family
:
ADH_N
(62)
Thermoanaerobacter brockii (Thermoanaerobium brockii)
(2)
1a
ADH_N-1ykfD01
D:24-135
1b
ADH_N-1ykfD02
D:24-135
1c
ADH_N-1ykfD03
D:24-135
1d
ADH_N-1ykfD04
D:24-135
Clan
:
NADP_Rossmann
(1239)
Family
:
ADH_zinc_N
(75)
Thermoanaerobacter brockii (Thermoanaerobium brockii)
(2)
2a
ADH_zinc_N-1ykfD05
D:177-310
2b
ADH_zinc_N-1ykfD06
D:177-310
2c
ADH_zinc_N-1ykfD07
D:177-310
2d
ADH_zinc_N-1ykfD08
D:177-310
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