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2DLD
Asym. Unit
Info
Asym.Unit (114 KB)
Biol.Unit 1 (108 KB)
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(1)
Title
:
D-LACTATE DEHYDROGENASE COMPLEXED WITH NADH AND OXAMATE
Authors
:
C. R. Dunn, J. J. Holbrook
Date
:
28 Oct 95 (Deposition) - 14 Mar 96 (Release) - 06 Nov 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Oxidoreductase (Choh(D)-Nad+(A))
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
N. Bernard, J. Delcour, A. Alvarez, A. Cortes, C. Willis, J. J. Holbroo
Dehydrogenases Engineering To Correct Substrate Inhibition In A Commercial Dehydrogenase
To Be Published
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
1b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
2a: OXAMIC ACID (OXMa)
2b: OXAMIC ACID (OXMb)
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Label:
No.
Name
Count
Type
Full Name
1
NAI
2
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
2
OXM
2
Ligand/Ion
OXAMIC ACID
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:154 , GLY A:155 , HIS A:156 , ILE A:157 , ASP A:176 , ILE A:177 , HIS A:206 , VAL A:207 , PRO A:208 , ASN A:213 , CYS A:234 , SER A:235 , ARG A:236 , THR A:261 , HIS A:297 , ALA A:299 , PHE A:337 , OXM A:402
BINDING SITE FOR RESIDUE NAI A 401
2
AC2
SOFTWARE
SER A:235 , ARG A:236 , HIS A:297 , NAI A:401
BINDING SITE FOR RESIDUE OXM A 402
3
AC3
SOFTWARE
THR B:154 , GLY B:155 , HIS B:156 , ILE B:157 , ASP B:176 , ILE B:177 , HIS B:206 , VAL B:207 , PRO B:208 , ASN B:213 , CYS B:234 , SER B:235 , ARG B:236 , ASP B:260 , THR B:261 , HIS B:297 , ALA B:299 , OXM B:402
BINDING SITE FOR RESIDUE NAI B 401
4
AC4
SOFTWARE
ARG B:236 , HIS B:297 , NAI B:401
BINDING SITE FOR RESIDUE OXM B 402
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: D_2_HYDROXYACID_DH_1 (A:149-176,B:149-176)
2: D_2_HYDROXYACID_DH_2 (A:196-218,B:196-218)
3: D_2_HYDROXYACID_DH_3 (A:225-241,B:225-241)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
D_2_HYDROXYACID_DH_1
PS00065
D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.
LDHD_LACHE
149-176
2
A:149-176
B:149-176
2
D_2_HYDROXYACID_DH_2
PS00670
D-isomer specific 2-hydroxyacid dehydrogenases signature 2.
LDHD_LACHE
196-218
2
A:196-218
B:196-218
3
D_2_HYDROXYACID_DH_3
PS00671
D-isomer specific 2-hydroxyacid dehydrogenases signature 3.
LDHD_LACHE
225-241
2
A:225-241
B:225-241
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2dlda2 (A:1-103,A:301-337)
1b: SCOP_d2dldb2 (B:1-103,B:301-337)
2a: SCOP_d2dlda1 (A:104-300)
2b: SCOP_d2dldb1 (B:104-300)
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Protein Domains
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Organisms
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(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Formate/glycerate dehydrogenase catalytic domain-like
(49)
Family
:
Formate/glycerate dehydrogenases, substrate-binding domain
(21)
Protein domain
:
D-lactate dehydrogenase
(3)
Lactobacillus helveticus [TaxId: 1587]
(3)
1a
d2dlda2
A:1-103,A:301-337
1b
d2dldb2
B:1-103,B:301-337
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Formate/glycerate dehydrogenases, NAD-domain
(49)
Protein domain
:
D-lactate dehydrogenase
(3)
Lactobacillus helveticus [TaxId: 1587]
(3)
2a
d2dlda1
A:104-300
2b
d2dldb1
B:104-300
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2dldA02 (A:104-299)
1b: CATH_2dldB02 (B:104-299)
1c: CATH_2dldA01 (A:1-103,A:301-336)
1d: CATH_2dldB01 (B:1-103,B:301-336)
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Organisms
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)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Lactobacillus helveticus. Organism_taxid: 1587
(1)
1a
2dldA02
A:104-299
1b
2dldB02
B:104-299
1c
2dldA01
A:1-103,A:301-336
1d
2dldB01
B:1-103,B:301-336
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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