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3VDR
Asym. Unit
Info
Asym.Unit (176 KB)
Biol.Unit 1 (168 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF D-3-HYDROXYBUTYRATE DEHYDROGENASE, PREPARED IN THE PRESENCE OF THE SUBSTRATE D-3-HYDROXYBUTYRATE AND NAD(+)
Authors
:
M. M. Hoque, S. Shimizu, E. C. M. Juan, Y. Sato, M. T. Hossain, T. Yamamoto S. Imamura, H. Amano, K. Suzuki, T. Sekiguchi, M. Tsunoda, A. Takenaka
Date
:
06 Jan 12 (Deposition) - 08 Feb 12 (Release) - 08 Feb 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Nad Dependent Enzymes, Ketone Bodies, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. M. Hoque, S. Shimizu, E. C. M. Juan, Y. Sato, M. T. Hossain, T. Yamamoto, S. Imamura, K. Suzuki, H. Amano, T. Sekiguchi, M. Tsunoda A. Takenaka
Structure Of D-3-Hydroxybutyrate Dehydrogenase Prepared In The Presence Of The Substrate D-3-Hydroxybutyrate And Nad+.
Acta Crystallogr. , Sect. F V. 65 331 2009
[
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Hetero Components
(6, 21)
Info
All Hetero Components
1a: (3R)-3-HYDROXYBUTANOIC ACID (3HRa)
1b: (3R)-3-HYDROXYBUTANOIC ACID (3HRb)
1c: (3R)-3-HYDROXYBUTANOIC ACID (3HRc)
1d: (3R)-3-HYDROXYBUTANOIC ACID (3HRd)
2a: ACETOACETIC ACID (AAEa)
2b: ACETOACETIC ACID (AAEb)
2c: ACETOACETIC ACID (AAEc)
2d: ACETOACETIC ACID (AAEd)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
4a: CHLORIDE ION (CLa)
4b: CHLORIDE ION (CLb)
4c: CHLORIDE ION (CLc)
5a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
5b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
5c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
5d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
6a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
6b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
6c: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIc)
6d: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAId)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3HR
4
Ligand/Ion
(3R)-3-HYDROXYBUTANOIC ACID
2
AAE
4
Ligand/Ion
ACETOACETIC ACID
3
CA
2
Ligand/Ion
CALCIUM ION
4
CL
3
Ligand/Ion
CHLORIDE ION
5
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
6
NAI
4
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:260 , HOH A:446 , HOH A:466 , VAL C:147 , ARG C:260
BINDING SITE FOR RESIDUE CA A 301
02
AC2
SOFTWARE
VAL A:150 , LYS A:219 , HOH C:410
BINDING SITE FOR RESIDUE CL A 302
03
AC3
SOFTWARE
GLY A:11 , THR A:13 , SER A:14 , GLY A:15 , ILE A:16 , PHE A:36 , ASP A:63 , LEU A:64 , ASN A:90 , ALA A:91 , GLY A:92 , LEU A:113 , ALA A:141 , TYR A:155 , LYS A:159 , PRO A:185 , GLY A:186 , VAL A:188 , THR A:190 , PRO A:191 , LEU A:192 , VAL A:193 , 3HR A:305 , AAE A:306 , ASP C:66
BINDING SITE FOR RESIDUE NAD A 303
04
AC4
SOFTWARE
GLY A:11 , THR A:13 , SER A:14 , GLY A:15 , ILE A:16 , PHE A:36 , ASP A:63 , LEU A:64 , ASN A:90 , ALA A:91 , GLY A:92 , LEU A:113 , ALA A:141 , SER A:142 , TYR A:155 , LYS A:159 , PRO A:185 , GLY A:186 , VAL A:188 , THR A:190 , PRO A:191 , LEU A:192 , VAL A:193 , 3HR A:305 , AAE A:306 , ASP C:66
BINDING SITE FOR RESIDUE NAI A 304
05
AC5
SOFTWARE
GLN A:94 , SER A:142 , HIS A:144 , LYS A:152 , TYR A:155 , TRP A:187 , LEU A:192 , GLN A:196 , TRP A:257 , NAD A:303 , NAI A:304
BINDING SITE FOR RESIDUE 3HR A 305
06
AC6
SOFTWARE
GLN A:94 , SER A:142 , HIS A:144 , LYS A:152 , TYR A:155 , GLY A:186 , TRP A:187 , LEU A:192 , GLN A:196 , TRP A:257 , NAD A:303 , NAI A:304
BINDING SITE FOR RESIDUE AAE A 306
07
AC7
SOFTWARE
ARG B:260 , ARG D:260 , HOH D:402
BINDING SITE FOR RESIDUE CA B 301
08
AC8
SOFTWARE
VAL B:150 , LYS B:219
BINDING SITE FOR RESIDUE CL B 302
09
AC9
SOFTWARE
GLY B:11 , THR B:13 , SER B:14 , GLY B:15 , ILE B:16 , PHE B:36 , ASP B:63 , LEU B:64 , ASN B:90 , ALA B:91 , GLY B:92 , LEU B:113 , ALA B:141 , SER B:142 , TYR B:155 , LYS B:159 , GLY B:186 , TRP B:187 , VAL B:188 , THR B:190 , PRO B:191 , LEU B:192 , VAL B:193 , 3HR B:305 , AAE B:306
BINDING SITE FOR RESIDUE NAD B 303
10
BC1
SOFTWARE
GLY B:11 , THR B:13 , SER B:14 , GLY B:15 , ILE B:16 , PHE B:36 , ASP B:63 , LEU B:64 , ASN B:90 , ALA B:91 , GLY B:92 , LEU B:113 , ALA B:141 , SER B:142 , TYR B:155 , LYS B:159 , GLY B:186 , TRP B:187 , VAL B:188 , THR B:190 , PRO B:191 , LEU B:192 , VAL B:193 , 3HR B:305 , AAE B:306
BINDING SITE FOR RESIDUE NAI B 304
11
BC2
SOFTWARE
GLN B:94 , SER B:142 , HIS B:144 , LYS B:152 , TYR B:155 , TRP B:187 , GLN B:196 , NAD B:303 , NAI B:304
BINDING SITE FOR RESIDUE 3HR B 305
12
BC3
SOFTWARE
GLN B:94 , SER B:142 , HIS B:144 , LYS B:152 , TYR B:155 , TRP B:187 , GLN B:196 , NAD B:303 , NAI B:304
BINDING SITE FOR RESIDUE AAE B 306
13
BC4
SOFTWARE
GLY C:11 , THR C:13 , SER C:14 , GLY C:15 , ILE C:16 , PHE C:36 , ASP C:63 , LEU C:64 , ASN C:90 , ALA C:91 , GLY C:92 , LEU C:113 , ALA C:141 , SER C:142 , TYR C:155 , LYS C:159 , PRO C:185 , GLY C:186 , TRP C:187 , VAL C:188 , THR C:190 , LEU C:192 , VAL C:193 , 3HR C:303 , AAE C:304 , HOH C:404 , HOH C:406 , HOH C:461
BINDING SITE FOR RESIDUE NAD C 301
14
BC5
SOFTWARE
GLY C:11 , THR C:13 , SER C:14 , GLY C:15 , ILE C:16 , PHE C:36 , ASP C:63 , LEU C:64 , ASN C:90 , ALA C:91 , GLY C:92 , LEU C:113 , ALA C:141 , SER C:142 , TYR C:155 , LYS C:159 , PRO C:185 , GLY C:186 , TRP C:187 , VAL C:188 , THR C:190 , LEU C:192 , VAL C:193 , 3HR C:303 , AAE C:304 , HOH C:404 , HOH C:406 , HOH C:461
BINDING SITE FOR RESIDUE NAI C 302
15
BC6
SOFTWARE
GLN C:94 , SER C:142 , HIS C:144 , LYS C:152 , TYR C:155 , GLN C:196 , NAD C:301 , NAI C:302
BINDING SITE FOR RESIDUE 3HR C 303
16
BC7
SOFTWARE
GLN C:94 , SER C:142 , HIS C:144 , LYS C:152 , TYR C:155 , GLY C:186 , GLN C:196 , NAD C:301 , NAI C:302
BINDING SITE FOR RESIDUE AAE C 304
17
BC8
SOFTWARE
VAL D:150 , LYS D:219
BINDING SITE FOR RESIDUE CL D 301
18
BC9
SOFTWARE
GLY D:11 , SER D:12 , THR D:13 , SER D:14 , GLY D:15 , ILE D:16 , PHE D:36 , ASP D:63 , LEU D:64 , ASN D:90 , ALA D:91 , GLY D:92 , LEU D:113 , ALA D:141 , SER D:142 , TYR D:155 , LYS D:159 , PRO D:185 , GLY D:186 , TRP D:187 , VAL D:188 , THR D:190 , LEU D:192 , VAL D:193 , 3HR D:304 , AAE D:305
BINDING SITE FOR RESIDUE NAD D 302
19
CC1
SOFTWARE
GLY D:11 , THR D:13 , SER D:14 , GLY D:15 , ILE D:16 , PHE D:36 , ASP D:63 , LEU D:64 , ASN D:90 , ALA D:91 , GLY D:92 , LEU D:113 , ALA D:141 , SER D:142 , TYR D:155 , LYS D:159 , PRO D:185 , GLY D:186 , TRP D:187 , VAL D:188 , THR D:190 , LEU D:192 , VAL D:193 , 3HR D:304 , AAE D:305
BINDING SITE FOR RESIDUE NAI D 303
20
CC2
SOFTWARE
GLN D:94 , SER D:142 , HIS D:144 , LYS D:152 , TYR D:155 , GLN D:196 , TRP D:257 , NAD D:302 , NAI D:303
BINDING SITE FOR RESIDUE 3HR D 304
21
CC3
SOFTWARE
GLN D:94 , SER D:142 , HIS D:144 , LYS D:152 , TYR D:155 , TRP D:187 , GLN D:196 , TRP D:257 , NAD D:302 , NAI D:303
BINDING SITE FOR RESIDUE AAE D 305
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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Exons
(0, 0)
Info
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All Exon Boundaries
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3vdra_ (A:)
1b: SCOP_d3vdrb_ (B:)
1c: SCOP_d3vdrc_ (C:)
1d: SCOP_d3vdrd_ (D:)
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Protein Domains
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Organisms
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(
)
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
:
automated matches
(114)
Alcaligenes faecalis [TaxId: 511]
(6)
1a
d3vdra_
A:
1b
d3vdrb_
B:
1c
d3vdrc_
C:
1d
d3vdrd_
D:
[
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CATH Domains
(0, 0 ; only for superseded entry 3EEW: 1,4)
Info
all CATH domains
1a: CATH_3eewA00 ()
1b: CATH_3eewB00 ()
1c: CATH_3eewC00 ()
1d: CATH_3eewD00 ()
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
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Sorry, no Info available
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