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1LDM
Asym. Unit
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Asym.Unit (64 KB)
Biol.Unit 1 (227 KB)
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(1)
Title
:
REFINED CRYSTAL STRUCTURE OF DOGFISH M4 APO-LACTATE DEHYDROGENASE
Authors
:
J. P. Griffith, M. G. Rossmann
Date
:
25 Nov 87 (Deposition) - 12 Jul 89 (Release) - 22 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A
Biol. Unit 1: A (4x)
Keywords
:
Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Abad-Zapatero, J. P. Griffith, J. L. Sussman, M. G. Rossmann
Refined Crystal Structure Of Dogfish M4 Apo-Lactate Dehydrogenase.
J. Mol. Biol. V. 198 445 1987
(for further references see the
PDB file header
)
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Hetero Components
(2, 3)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2a: OXAMIC ACID (OXMa)
2b: OXAMIC ACID (OXMb)
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Label:
No.
Name
Count
Type
Full Name
1
NAD
1
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
OXM
2
Ligand/Ion
OXAMIC ACID
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
VAL A:28 , GLY A:29 , ASP A:52 , VAL A:53 , MET A:54 , GLU A:55 , ASP A:56 , LYS A:57 , LEU A:58 , LYS A:59 , GLY A:60 , GLU A:61 , SER A:79 , LYS A:81 , ASP A:82 , TYR A:83 , THR A:95 , ALA A:96 , ALA A:98 , ARG A:99 , VAL A:136 , SER A:137 , ASN A:138 , SER A:161 , HIS A:193 , LEU A:241 , LYS A:242 , TYR A:244 , SER A:246 , OXM A:331 , HOH A:347 , HOH A:353 , HOH A:359 , HOH A:373 , HOH A:384 , HOH A:493 , HOH A:496 , HOH A:497
BINDING SITE FOR RESIDUE NAD A 330
2
AC2
SOFTWARE
ARG A:106 , HIS A:193 , ALA A:235 , NAD A:330
BINDING SITE FOR RESIDUE OXM A 331
3
AC3
SOFTWARE
GLN A:111 , ARG A:171 , HIS A:186 , VAL A:291 , HOH A:335 , HOH A:424 , HOH A:439
BINDING SITE FOR RESIDUE OXM A 332
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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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: L_LDH (A:190-196)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
L_LDH
PS00064
L-lactate dehydrogenase active site.
LDHA_SQUAC
191-197
1
A:190-196
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Exons
(0, 0)
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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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1ldma2 (A:161-329)
2a: SCOP_d1ldma1 (A:1-160)
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
LDH C-terminal domain-like
(172)
Superfamily
:
LDH C-terminal domain-like
(172)
Family
:
Lactate & malate dehydrogenases, C-terminal domain
(125)
Protein domain
:
Lactate dehydrogenase
(55)
Dogfish (Squalus acanthias) [TaxId: 7797]
(3)
1a
d1ldma2
A:161-329
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
:
LDH N-terminal domain-like
(117)
Protein domain
:
Lactate dehydrogenase
(53)
Dogfish (Squalus acanthias) [TaxId: 7797]
(3)
2a
d1ldma1
A:1-160
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1ldmA01 (A:1-162)
2a: CATH_1ldmA02 (A:163-329)
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)
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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)
Spiny dogfish (Squalus acanthias)
(4)
1a
1ldmA01
A:1-162
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
(116)
Homologous Superfamily
:
L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2
(116)
Spiny dogfish (Squalus acanthias)
(4)
2a
1ldmA02
A:163-329
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Ldh_1_C_1ldmA01 (A:163-329)
2a: PFAM_Ldh_1_N_1ldmA02 (A:21-161)
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Clans
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Organisms
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)
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)
Clan
:
LDH_C
(56)
Family
:
Ldh_1_C
(51)
Squalus acanthias (Spiny dogfish)
(2)
1a
Ldh_1_C-1ldmA01
A:163-329
Clan
:
NADP_Rossmann
(1239)
Family
:
Ldh_1_N
(51)
Squalus acanthias (Spiny dogfish)
(2)
2a
Ldh_1_N-1ldmA02
A:21-161
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