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1GEG
Biol. Unit 1
Info
Asym.Unit (328 KB)
Biol.Unit 1 (162 KB)
Biol.Unit 2 (164 KB)
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(1)
Title
:
CRYATAL STRUCTURE ANALYSIS OF MESO-2,3-BUTANEDIOL DEHYDROGENASE
Authors
:
M. Otagiri, G. Kurisu, S. Ui, M. Kusunoki
Date
:
10 Nov 00 (Deposition) - 28 Feb 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Sdr Family, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Otagiri, G. Kurisu, S. Ui, Y. Takusagawa, M. Ohkuma, T. Kudo, M. Kusunoki
Crystal Structure Of Meso-2, 3-Butanediol Dehydrogenase In A Complex With Nad+ And Inhibitor Mercaptoethanol At 1. 7 A Resolution For Understanding Of Chiral Substrate Recognition Mechanisms.
J. Biochem. (Tokyo) V. 129 205 2001
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: BETA-MERCAPTOETHANOL (BMEa)
1b: BETA-MERCAPTOETHANOL (BMEb)
1c: BETA-MERCAPTOETHANOL (BMEc)
1d: BETA-MERCAPTOETHANOL (BMEd)
1e: BETA-MERCAPTOETHANOL (BMEe)
1f: BETA-MERCAPTOETHANOL (BMEf)
1g: BETA-MERCAPTOETHANOL (BMEg)
1h: BETA-MERCAPTOETHANOL (BMEh)
2a: ALPHA-D-GLUCOSE (GLCa)
2b: ALPHA-D-GLUCOSE (GLCb)
2c: ALPHA-D-GLUCOSE (GLCc)
2d: ALPHA-D-GLUCOSE (GLCd)
2e: ALPHA-D-GLUCOSE (GLCe)
2f: ALPHA-D-GLUCOSE (GLCf)
2g: ALPHA-D-GLUCOSE (GLCg)
2h: ALPHA-D-GLUCOSE (GLCh)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
4b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
4c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
4d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
4e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
4f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
4g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
4h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BME
4
Ligand/Ion
BETA-MERCAPTOETHANOL
2
GLC
4
Ligand/Ion
ALPHA-D-GLUCOSE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
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]
Sites
(13, 13)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC9 (SOFTWARE)
11: CC1 (SOFTWARE)
12: CC2 (SOFTWARE)
13: CC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:63 , ASP A:64 , PHE A:67 , GLU A:123 , HOH A:2062
BINDING SITE FOR RESIDUE GLC A 302
02
AC2
SOFTWARE
ARG B:63 , ASP B:64 , PHE B:67 , GLU B:123
BINDING SITE FOR RESIDUE GLC B 303
03
AC3
SOFTWARE
ARG C:63 , ASP C:64 , PHE C:67 , GLU C:123 , HOH C:3542
BINDING SITE FOR RESIDUE GLC C 304
04
AC4
SOFTWARE
ARG D:63 , ASP D:64 , PHE D:67 , GLU D:123 , HOH D:4528
BINDING SITE FOR RESIDUE GLC D 305
05
AC9
SOFTWARE
HOH A:2108 , HOH A:2109 , HOH A:2110 , HOH A:2111 , HOH A:2112
BINDING SITE FOR RESIDUE MG A 2000
06
BC1
SOFTWARE
GLY A:9 , GLN A:12 , GLY A:13 , ILE A:14 , ASP A:33 , TYR A:34 , VAL A:58 , ASP A:59 , VAL A:60 , ASN A:86 , ALA A:87 , ILE A:109 , ALA A:137 , CYS A:138 , SER A:139 , TYR A:152 , LYS A:156 , PRO A:182 , GLY A:183 , VAL A:185 , THR A:187 , PRO A:188 , MET A:189 , BME A:1462 , HOH A:2024 , HOH A:2042 , HOH A:2102
BINDING SITE FOR RESIDUE NAD A 2001
07
BC2
SOFTWARE
GLY B:9 , GLN B:12 , GLY B:13 , ILE B:14 , ASP B:33 , TYR B:34 , VAL B:58 , ASP B:59 , VAL B:60 , ASN B:86 , ALA B:87 , ILE B:109 , ALA B:137 , CYS B:138 , SER B:139 , TYR B:152 , LYS B:156 , PRO B:182 , GLY B:183 , VAL B:185 , THR B:187 , PRO B:188 , MET B:189 , BME B:2462 , HOH B:2468 , HOH B:2482 , HOH B:2486 , HOH B:2553 , HOH B:2557
BINDING SITE FOR RESIDUE NAD B 2002
08
BC3
SOFTWARE
GLY C:9 , GLN C:12 , ILE C:14 , ASP C:33 , TYR C:34 , VAL C:58 , ASP C:59 , VAL C:60 , ASN C:86 , GLY C:88 , ILE C:109 , ALA C:137 , CYS C:138 , SER C:139 , TYR C:152 , LYS C:156 , PRO C:182 , GLY C:183 , VAL C:185 , THR C:187 , PRO C:188 , MET C:189 , BME C:3462 , HOH C:3490 , HOH C:3492 , HOH C:3520 , HOH C:3552 , HOH C:3553 , HOH C:3554 , HOH C:3555
BINDING SITE FOR RESIDUE NAD C 305
09
BC4
SOFTWARE
GLY D:9 , GLN D:12 , GLY D:13 , ILE D:14 , ASP D:33 , TYR D:34 , VAL D:58 , ASP D:59 , VAL D:60 , ASN D:86 , ILE D:109 , ALA D:137 , CYS D:138 , SER D:139 , TYR D:152 , LYS D:156 , PRO D:182 , GLY D:183 , VAL D:185 , THR D:187 , PRO D:188 , MET D:189 , BME D:4462 , HOH D:4482 , HOH D:4484 , HOH D:4487
BINDING SITE FOR RESIDUE NAD D 306
10
BC9
SOFTWARE
SER A:139 , GLN A:140 , TYR A:152 , PRO A:182 , GLY A:183 , NAD A:2001
BINDING SITE FOR RESIDUE BME A 1462
11
CC1
SOFTWARE
SER B:139 , GLN B:140 , TYR B:152 , PRO B:182 , GLY B:183 , NAD B:2002
BINDING SITE FOR RESIDUE BME B 2462
12
CC2
SOFTWARE
SER C:139 , GLN C:140 , TYR C:152 , PRO C:182 , GLY C:183 , NAD C:305
BINDING SITE FOR RESIDUE BME C 3462
13
CC3
SOFTWARE
SER D:139 , GLN D:140 , TYR D:152 , PRO D:182 , GLY D:183 , NAD D:306
BINDING SITE FOR RESIDUE BME D 4462
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ADH_SHORT (A:139-167,B:139-167,C:139-167,D:13...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADH_SHORT
PS00061
Short-chain dehydrogenases/reductases family signature.
BUDC_KLEPN
139-167
4
A:139-167
B:139-167
C:139-167
D:139-167
-
-
-
-
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Exons
(0, 0)
Info
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Note:
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
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1gega_ (A:)
1b: SCOP_d1gegb_ (B:)
1c: SCOP_d1gegc_ (C:)
1d: SCOP_d1gegd_ (D:)
1e: SCOP_d1gege_ (E:)
1f: SCOP_d1gegf_ (F:)
1g: SCOP_d1gegg_ (G:)
1h: SCOP_d1gegh_ (H:)
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(
)
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)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
:
Tyrosine-dependent oxidoreductases
(503)
Protein domain
:
meso-2,3-butanediol dehydrogenase
(1)
Klebsiella pneumoniae [TaxId: 573]
(1)
1a
d1gega_
A:
1b
d1gegb_
B:
1c
d1gegc_
C:
1d
d1gegd_
D:
1e
d1gege_
E:
1f
d1gegf_
F:
1g
d1gegg_
G:
1h
d1gegh_
H:
[
close SCOP info
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1gegA00 (A:2-256)
1b: CATH_1gegB00 (B:2-256)
1c: CATH_1gegC00 (C:2-256)
1d: CATH_1gegD00 (D:2-256)
1e: CATH_1gegF00 (F:2-256)
1f: CATH_1gegG00 (G:2-256)
1g: CATH_1gegH00 (H:2-256)
1h: CATH_1gegE00 (E:1-256)
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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)
Klebsiella pneumoniae. Organism_taxid: 573.
(2)
1a
1gegA00
A:2-256
1b
1gegB00
B:2-256
1c
1gegC00
C:2-256
1d
1gegD00
D:2-256
1e
1gegF00
F:2-256
1f
1gegG00
G:2-256
1g
1gegH00
H:2-256
1h
1gegE00
E:1-256
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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