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3A28
Asym. Unit
Info
Asym.Unit (351 KB)
Biol.Unit 1 (175 KB)
Biol.Unit 2 (174 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF L-2,3-BUTANEDIOL DEHYDROGENASE
Authors
:
M. Otagiri, G. Kurisu, S. Ui, M. Kusunoki
Date
:
02 May 09 (Deposition) - 15 Dec 09 (Release) - 22 Jan 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
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
:
Chiral Substrate Recognition, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Otagiri, S. Ui, Y. Takusagawa, T. Ohtsuki, G. Kurisu, M. Kusunoki
Structural Basis For Chiral Substrate Recognition By Two 2, 3-Butanediol Dehydrogenases
Febs Lett. V. 584 219 2010
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close entry info
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Hetero Components
(3, 20)
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: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
3b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
3d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
3e: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADe)
3f: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADf)
3g: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADg)
3h: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BME
8
Ligand/Ion
BETA-MERCAPTOETHANOL
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
NAD
8
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
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Sites
(19, 19)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY C:9 , GLN C:12 , GLY C:13 , ILE C:14 , ASP C:33 , GLN C:37 , LEU C:60 , ASP C:61 , VAL C:62 , ASN C:88 , ALA C:139 , ALA C:140 , SER C:141 , TYR C:154 , LYS C:158 , PRO C:184 , GLY C:185 , VAL C:187 , THR C:189 , MET C:191 , TRP C:192 , HOH C:266 , HOH C:545 , HOH C:683 , HOH C:1520 , HOH C:1635 , HOH C:1636 , BME C:4462
BINDING SITE FOR RESIDUE NAD C 4300
02
AC2
SOFTWARE
SER C:141 , TYR C:154 , GLY C:185 , ILE C:186 , TRP C:192 , NAD C:4300
BINDING SITE FOR RESIDUE BME C 4462
03
AC3
SOFTWARE
HOH B:1094 , HOH C:655
BINDING SITE FOR RESIDUE MG C 804
04
AC4
SOFTWARE
GLY D:9 , GLN D:12 , GLY D:13 , ILE D:14 , ASP D:33 , LEU D:34 , GLN D:37 , LEU D:60 , ASP D:61 , VAL D:62 , ASN D:88 , ALA D:89 , ALA D:139 , ALA D:140 , SER D:141 , TYR D:154 , LYS D:158 , PRO D:184 , GLY D:185 , VAL D:187 , THR D:189 , MET D:191 , TRP D:192 , HOH D:391 , HOH D:793 , HOH D:1666 , HOH D:1667 , HOH D:1668 , BME D:5462
BINDING SITE FOR RESIDUE NAD D 5300
05
AC5
SOFTWARE
SER D:141 , TYR D:154 , GLY D:185 , ILE D:186 , TRP D:192 , NAD D:5300
BINDING SITE FOR RESIDUE BME D 5462
06
AC6
SOFTWARE
HOH A:668 , HOH D:790
BINDING SITE FOR RESIDUE MG D 805
07
AC7
SOFTWARE
GLN A:12 , GLY A:13 , ILE A:14 , ASP A:33 , GLN A:37 , LEU A:60 , ASP A:61 , VAL A:62 , ASN A:88 , ALA A:89 , GLY A:90 , VAL A:111 , ALA A:139 , ALA A:140 , SER A:141 , TYR A:154 , LYS A:158 , PRO A:184 , GLY A:185 , VAL A:187 , THR A:189 , MET A:191 , TRP A:192 , HOH A:399 , HOH A:639 , HOH A:813 , HOH A:1084 , HOH A:1321 , HOH A:1574 , BME A:2462
BINDING SITE FOR RESIDUE NAD A 2300
08
AC8
SOFTWARE
SER A:141 , TYR A:154 , GLY A:185 , ILE A:186 , TRP A:192 , NAD A:2300
BINDING SITE FOR RESIDUE BME A 2462
09
AC9
SOFTWARE
GLY B:9 , GLN B:12 , GLY B:13 , ILE B:14 , ASP B:33 , GLN B:37 , LEU B:60 , ASP B:61 , VAL B:62 , THR B:63 , ASN B:88 , ALA B:89 , ALA B:139 , ALA B:140 , SER B:141 , TYR B:154 , LYS B:158 , PRO B:184 , GLY B:185 , VAL B:187 , THR B:189 , MET B:191 , TRP B:192 , HOH B:262 , HOH B:368 , HOH B:400 , HOH B:954 , HOH B:1589 , BME B:3462
BINDING SITE FOR RESIDUE NAD B 3300
10
BC1
SOFTWARE
SER B:141 , ILE B:142 , TYR B:154 , GLY B:185 , ILE B:186 , TRP B:192 , NAD B:3300
BINDING SITE FOR RESIDUE BME B 3462
11
BC2
SOFTWARE
GLY E:9 , GLN E:12 , GLY E:13 , ILE E:14 , ASP E:33 , LEU E:34 , GLN E:37 , LEU E:60 , ASP E:61 , VAL E:62 , ASN E:88 , ALA E:140 , SER E:141 , TYR E:154 , LYS E:158 , PRO E:184 , GLY E:185 , VAL E:187 , THR E:189 , MET E:191 , TRP E:192 , HOH E:416 , HOH E:958 , HOH E:1021 , HOH E:1697 , HOH E:1698 , BME E:6462
BINDING SITE FOR RESIDUE NAD E 6300
12
BC3
SOFTWARE
SER E:141 , TYR E:154 , GLY E:185 , ILE E:186 , TRP E:192 , NAD E:6300
BINDING SITE FOR RESIDUE BME E 6462
13
BC4
SOFTWARE
GLY F:9 , GLN F:12 , GLY F:13 , ILE F:14 , ASP F:33 , LEU F:34 , GLN F:37 , LEU F:60 , ASP F:61 , VAL F:62 , ASN F:88 , ALA F:139 , ALA F:140 , SER F:141 , TYR F:154 , LYS F:158 , PRO F:184 , GLY F:185 , VAL F:187 , THR F:189 , MET F:191 , TRP F:192 , HOH F:340 , HOH F:413 , HOH F:513 , HOH F:959 , HOH F:1695 , HOH F:1696 , BME F:7462
BINDING SITE FOR RESIDUE NAD F 7300
14
BC5
SOFTWARE
SER F:141 , TYR F:154 , GLY F:185 , ILE F:186 , TRP F:192 , NAD F:7300
BINDING SITE FOR RESIDUE BME F 7462
15
BC6
SOFTWARE
HOH F:906
BINDING SITE FOR RESIDUE MG F 948
16
BC7
SOFTWARE
GLN G:12 , ILE G:14 , ASP G:33 , LEU G:34 , GLN G:37 , LEU G:60 , ASP G:61 , VAL G:62 , ASN G:88 , ALA G:139 , ALA G:140 , SER G:141 , TYR G:154 , LYS G:158 , PRO G:184 , GLY G:185 , VAL G:187 , THR G:189 , MET G:191 , TRP G:192 , HOH G:450 , HOH G:783 , HOH G:1326 , HOH G:1691 , HOH G:1693 , HOH G:1732 , BME G:8462
BINDING SITE FOR RESIDUE NAD G 8300
17
BC8
SOFTWARE
SER G:141 , TYR G:154 , GLY G:185 , ILE G:186 , TRP G:192 , NAD G:8300
BINDING SITE FOR RESIDUE BME G 8462
18
BC9
SOFTWARE
GLY H:9 , GLN H:12 , GLY H:13 , ILE H:14 , ASP H:33 , GLN H:37 , LEU H:60 , ASP H:61 , VAL H:62 , ASN H:88 , ALA H:89 , VAL H:111 , ALA H:139 , ALA H:140 , SER H:141 , TYR H:154 , LYS H:158 , PRO H:184 , GLY H:185 , VAL H:187 , THR H:189 , MET H:191 , TRP H:192 , HOH H:265 , HOH H:548 , HOH H:1010 , HOH H:1689 , HOH H:1713 , BME H:9462
BINDING SITE FOR RESIDUE NAD H 9300
19
CC1
SOFTWARE
SER H:141 , TYR H:154 , GLY H:185 , ILE H:186 , TRP H:192 , NAD H:9300
BINDING SITE FOR RESIDUE BME H 9462
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: ADH_SHORT (A:141-169,B:141-169,C:141-169,D:14...)
;
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_CORGT
141-169
8
A:141-169
B:141-169
C:141-169
D:141-169
E:141-169
F:141-169
G:141-169
H:141-169
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_d3a28a_ (A:)
1b: SCOP_d3a28b_ (B:)
1c: SCOP_d3a28c_ (C:)
1d: SCOP_d3a28d_ (D:)
1e: SCOP_d3a28e_ (E:)
1f: SCOP_d3a28f_ (F:)
1g: SCOP_d3a28g_ (G:)
1h: SCOP_d3a28h_ (H:)
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Classes
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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
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Brevibacterium saccharolyticum [TaxId: 1718]
(1)
1a
d3a28a_
A:
1b
d3a28b_
B:
1c
d3a28c_
C:
1d
d3a28d_
D:
1e
d3a28e_
E:
1f
d3a28f_
F:
1g
d3a28g_
G:
1h
d3a28h_
H:
[
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]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_3a28A00 (A:2-258)
1b: CATH_3a28B00 (B:2-258)
1c: CATH_3a28C00 (C:2-258)
1d: CATH_3a28D00 (D:2-258)
1e: CATH_3a28E00 (E:2-258)
1f: CATH_3a28F00 (F:2-258)
1g: CATH_3a28G00 (G:2-258)
1h: CATH_3a28H00 (H:2-258)
View:
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Brevibacterium saccharolyticum. Organism_taxid: 1718. Strain: c-1012.
(1)
1a
3a28A00
A:2-258
1b
3a28B00
B:2-258
1c
3a28C00
C:2-258
1d
3a28D00
D:2-258
1e
3a28E00
E:2-258
1f
3a28F00
F:2-258
1g
3a28G00
G:2-258
1h
3a28H00
H:2-258
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain E
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Chain H
Asymmetric Unit 1
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