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1GEG
Asym. Unit
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
(4, 28)
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
8
Ligand/Ion
BETA-MERCAPTOETHANOL
2
GLC
8
Ligand/Ion
ALPHA-D-GLUCOSE
3
MG
4
Ligand/Ion
MAGNESIUM ION
4
NAD
8
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(25, 25)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
View:
Select:
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
AC5
SOFTWARE
ARG E:63 , ASP E:64 , PHE E:67 , GLU E:123 , HOH E:5539
BINDING SITE FOR RESIDUE GLC E 306
06
AC6
SOFTWARE
PHE F:67 , GLU F:123 , HOH F:6491 , HOH F:6536
BINDING SITE FOR RESIDUE GLC F 307
07
AC7
SOFTWARE
ARG G:63 , ASP G:64 , PHE G:67 , GLU G:123
BINDING SITE FOR RESIDUE GLC G 308
08
AC8
SOFTWARE
ARG H:63 , ASP H:64 , PHE H:67 , GLU H:123 , HOH H:8509 , HOH H:8518
BINDING SITE FOR RESIDUE GLC H 309
09
AC9
SOFTWARE
HOH A:2108 , HOH A:2109 , HOH A:2110 , HOH A:2111 , HOH A:2112
BINDING SITE FOR RESIDUE MG A 2000
10
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
11
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
12
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
13
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
14
BC5
SOFTWARE
GLY E:9 , GLN E:12 , GLY E:13 , ILE E:14 , ASP E:33 , TYR E:34 , VAL E:58 , ASP E:59 , VAL E:60 , ASN E:86 , ALA E:87 , ILE E:109 , ALA E:137 , CYS E:138 , SER E:139 , TYR E:152 , LYS E:156 , PRO E:182 , GLY E:183 , VAL E:185 , THR E:187 , PRO E:188 , MET E:189 , BME E:5462 , HOH E:5547
BINDING SITE FOR RESIDUE NAD E 307
15
BC6
SOFTWARE
GLY F:9 , GLN F:12 , GLY F:13 , ILE F:14 , ASP F:33 , TYR F:34 , VAL F:58 , ASP F:59 , VAL F:60 , ASN F:86 , ALA F:87 , ILE F:109 , ALA F:137 , CYS F:138 , SER F:139 , TYR F:152 , LYS F:156 , PRO F:182 , GLY F:183 , VAL F:185 , THR F:187 , PRO F:188 , MET F:189 , BME F:6462 , HOH F:6485 , HOH F:6537
BINDING SITE FOR RESIDUE NAD F 308
16
BC7
SOFTWARE
GLY G:9 , GLN G:12 , GLY G:13 , ILE G:14 , ASP G:33 , TYR G:34 , VAL G:58 , ASP G:59 , VAL G:60 , ASN G:86 , ALA G:87 , ILE G:109 , ALA G:137 , CYS G:138 , SER G:139 , TYR G:152 , LYS G:156 , PRO G:182 , GLY G:183 , VAL G:185 , THR G:187 , PRO G:188 , MET G:189 , BME G:7462 , HOH G:7484 , HOH G:7572 , HOH G:7574
BINDING SITE FOR RESIDUE NAD G 2003
17
BC8
SOFTWARE
GLY H:9 , GLN H:12 , GLY H:13 , ILE H:14 , ASP H:33 , TYR H:34 , VAL H:58 , ASP H:59 , VAL H:60 , ASN H:86 , ILE H:109 , ALA H:137 , CYS H:138 , SER H:139 , TYR H:152 , LYS H:156 , PRO H:182 , GLY H:183 , VAL H:185 , THR H:187 , PRO H:188 , MET H:189 , BME H:8462 , HOH H:8468 , HOH H:8487 , HOH H:8555 , HOH H:8556 , HOH H:8557
BINDING SITE FOR RESIDUE NAD H 2004
18
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
19
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
20
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
21
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
22
CC4
SOFTWARE
SER E:139 , GLN E:140 , TYR E:152 , PRO E:182 , GLY E:183 , NAD E:307
BINDING SITE FOR RESIDUE BME E 5462
23
CC5
SOFTWARE
SER F:139 , GLN F:140 , TYR F:152 , PRO F:182 , GLY F:183 , NAD F:308
BINDING SITE FOR RESIDUE BME F 6462
24
CC6
SOFTWARE
SER G:139 , GLN G:140 , TYR G:152 , PRO G:182 , GLY G:183 , NAD G:2003
BINDING SITE FOR RESIDUE BME G 7462
25
CC7
SOFTWARE
SER H:139 , GLN H:140 , TYR H:152 , PRO H:182 , GLY H:183 , NAD H:2004
BINDING SITE FOR RESIDUE BME H 8462
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: ADH_SHORT (A:139-167,B:139-167,C:139-167,D:13...)
;
View:
Select:
Label:
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
8
A:139-167
B:139-167
C:139-167
D:139-167
E:139-167
F:139-167
G:139-167
H:139-167
[
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Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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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Classes
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)
(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
]
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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Homologous Superfamilies
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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
[
close CATH info
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Pfam Domains
(0, 0)
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all PFAM domains
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