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2V7P
Asym. Unit
Info
Asym.Unit (203 KB)
Biol.Unit 1 (196 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF LACTATE DEHYDROGENASE FROM THERMUS THERMOPHILUS HB8 (HOLO FORM)
Authors
:
N. Coquelle, E. Fioravanti, M. Weik, F. Vellieux
Date
:
31 Jul 07 (Deposition) - 25 Sep 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Oxidoreductase, Phosphorylation, Nad, Lactate, Cytoplasm, Glycolysis, Thermophile
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Reference
:
N. Coquelle, E. Fioravanti, M. Weik, F. Vellieux, D. Madern
Activity, Stability And Structural Studies Of Lactate Dehydrogenases Adapted To Extreme Thermal Environments.
J. Mol. Biol. V. 374 547 2007
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
1b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
1c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
1d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
2a: OXAMIC ACID (OXMa)
2b: OXAMIC ACID (OXMb)
2c: OXAMIC ACID (OXMc)
2d: OXAMIC ACID (OXMd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2
OXM
4
Ligand/Ion
OXAMIC ACID
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:102 , ARG A:109 , ASN A:140 , LEU A:167 , ARG A:171 , HIS A:195 , ALA A:236 , THR A:246 , NAD A:1332 , HOH A:2146
BINDING SITE FOR RESIDUE OXM A 501
2
AC2
SOFTWARE
GLY A:28 , GLY A:30 , MET A:31 , VAL A:32 , ASP A:53 , LEU A:54 , LEU A:58 , TYR A:85 , ALA A:98 , GLY A:99 , VAL A:100 , ALA A:101 , GLN A:102 , VAL A:123 , ALA A:138 , THR A:139 , ASN A:140 , SER A:163 , HIS A:195 , THR A:246 , ILE A:250 , OXM A:501 , HOH A:2072 , HOH A:2110 , HOH A:2142 , HOH A:2143 , HOH A:2144 , HOH A:2145 , HOH A:2146 , HOH A:2147 , GLN C:111 , HOH C:2050
BINDING SITE FOR RESIDUE NAD A1332
3
AC3
SOFTWARE
ASN B:140 , LEU B:167 , ARG B:171 , HIS B:195 , ALA B:236 , THR B:246 , NAD B:1332 , HOH B:2130 , HOH B:2131
BINDING SITE FOR RESIDUE OXM B 501
4
AC4
SOFTWARE
GLY B:30 , MET B:31 , VAL B:32 , ASP B:53 , LEU B:54 , LEU B:58 , ALA B:97 , ALA B:98 , VAL B:119 , VAL B:123 , ALA B:138 , THR B:139 , ASN B:140 , SER B:163 , LEU B:167 , HIS B:195 , THR B:246 , ILE B:250 , OXM B:501 , HOH B:2031 , HOH B:2053 , HOH B:2100 , HOH B:2130 , HOH B:2132 , HOH B:2133 , HOH B:2135 , HOH B:2136
BINDING SITE FOR RESIDUE NAD B1332
5
AC5
SOFTWARE
GLN C:102 , ARG C:109 , ASN C:140 , LEU C:167 , ARG C:171 , HIS C:195 , ALA C:236 , THR C:246 , NAD C:1332
BINDING SITE FOR RESIDUE OXM C 501
6
AC6
SOFTWARE
GLY C:30 , MET C:31 , VAL C:32 , ASP C:53 , LEU C:54 , LEU C:58 , TYR C:85 , ALA C:98 , GLY C:99 , VAL C:100 , ALA C:101 , VAL C:123 , ALA C:138 , THR C:139 , ASN C:140 , SER C:163 , HIS C:195 , THR C:246 , ILE C:250 , OXM C:501 , HOH C:2004 , HOH C:2076 , HOH C:2109 , HOH C:2149 , HOH C:2150 , HOH C:2151
BINDING SITE FOR RESIDUE NAD C1332
7
AC7
SOFTWARE
ASN D:140 , LEU D:167 , ARG D:171 , HIS D:195 , ALA D:236 , THR D:246 , NAD D:1332
BINDING SITE FOR RESIDUE OXM D 501
8
AC8
SOFTWARE
GLY D:30 , MET D:31 , VAL D:32 , ASP D:53 , LEU D:54 , LEU D:58 , TYR D:85 , ALA D:97 , ALA D:98 , GLY D:99 , VAL D:119 , ALA D:138 , THR D:139 , ASN D:140 , SER D:163 , HIS D:195 , THR D:246 , ILE D:250 , OXM D:501 , HOH D:2030 , HOH D:2098 , HOH D:2099 , HOH D:2100
BINDING SITE FOR RESIDUE NAD D1332
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: L_LDH (A:192-198,B:192-198,C:192-198,D:19...)
;
View:
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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.
LDH_THET8
169-175
4
A:192-198
B:192-198
C:192-198
D:192-198
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Exons
(0, 0)
Info
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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, 8)
Info
All SCOP Domains
1a: SCOP_d2v7pa2 (A:165-331)
1b: SCOP_d2v7pb2 (B:165-331)
1c: SCOP_d2v7pc2 (C:165-331)
1d: SCOP_d2v7pd2 (D:165-331)
2a: SCOP_d2v7pa1 (A:22-164)
2b: SCOP_d2v7pb1 (B:22-164)
2c: SCOP_d2v7pc1 (C:22-164)
2d: SCOP_d2v7pd1 (D:22-164)
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Protein Domains
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)
Organisms
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)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
LDH C-terminal domain-like
(172)
Superfamily
:
LDH C-terminal domain-like
(172)
Family
:
automated matches
(38)
Protein domain
:
automated matches
(38)
Thermus thermophilus HB8 [TaxId: 300852]
(7)
1a
d2v7pa2
A:165-331
1b
d2v7pb2
B:165-331
1c
d2v7pc2
C:165-331
1d
d2v7pd2
D:165-331
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)
Thermus thermophilus HB8 [TaxId: 300852]
(16)
2a
d2v7pa1
A:22-164
2b
d2v7pb1
B:22-164
2c
d2v7pc1
C:22-164
2d
d2v7pd1
D:22-164
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2v7pA01 (A:22-164)
1b: CATH_2v7pC01 (C:22-164)
1c: CATH_2v7pD01 (D:22-164)
1d: CATH_2v7pB01 (B:22-164)
2a: CATH_2v7pA02 (A:165-331)
2b: CATH_2v7pB02 (B:165-331)
2c: CATH_2v7pC02 (C:165-331)
2d: CATH_2v7pD02 (D:165-331)
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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)
Thermus thermophilus. Organism_taxid: 300852. Strain: hb8.
(3)
1a
2v7pA01
A:22-164
1b
2v7pC01
C:22-164
1c
2v7pD01
D:22-164
1d
2v7pB01
B:22-164
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)
Thermus thermophilus. Organism_taxid: 300852. Strain: hb8.
(2)
2a
2v7pA02
A:165-331
2b
2v7pB02
B:165-331
2c
2v7pC02
C:165-331
2d
2v7pD02
D:165-331
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Ldh_1_C_2v7pD01 (D:165-328)
1b: PFAM_Ldh_1_C_2v7pD02 (D:165-328)
1c: PFAM_Ldh_1_C_2v7pD03 (D:165-328)
1d: PFAM_Ldh_1_C_2v7pD04 (D:165-328)
2a: PFAM_Ldh_1_N_2v7pD05 (D:22-163)
2b: PFAM_Ldh_1_N_2v7pD06 (D:22-163)
2c: PFAM_Ldh_1_N_2v7pD07 (D:22-163)
2d: PFAM_Ldh_1_N_2v7pD08 (D:22-163)
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Clan
:
LDH_C
(56)
Family
:
Ldh_1_C
(51)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(3)
1a
Ldh_1_C-2v7pD01
D:165-328
1b
Ldh_1_C-2v7pD02
D:165-328
1c
Ldh_1_C-2v7pD03
D:165-328
1d
Ldh_1_C-2v7pD04
D:165-328
Clan
:
NADP_Rossmann
(1239)
Family
:
Ldh_1_N
(51)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
(3)
2a
Ldh_1_N-2v7pD05
D:22-163
2b
Ldh_1_N-2v7pD06
D:22-163
2c
Ldh_1_N-2v7pD07
D:22-163
2d
Ldh_1_N-2v7pD08
D:22-163
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