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1I10
Biol. Unit 2
Info
Asym.Unit (445 KB)
Biol.Unit 1 (223 KB)
Biol.Unit 2 (219 KB)
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Title
:
HUMAN MUSCLE L-LACTATE DEHYDROGENASE M CHAIN, TERNARY COMPLEX WITH NADH AND OXAMATE
Authors
:
J. A. Read, V. J. Winter, C. M. Eszes, R. B. Sessions, R. L. Brady
Date
:
30 Jan 01 (Deposition) - 28 Mar 01 (Release) - 12 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
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
:
Dehydrogenase, Rossmann Fold, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. A. Read, V. J. Winter, C. M. Eszes, R. B. Sessions, R. L. Brady
Structural Basis For Altered Activity Of M- And H-Isozyme Forms Of Human Lactate Dehydrogenase.
Proteins V. 43 175 2001
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
1h: ACETATE ION (ACTh)
2a: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIa)
2b: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIb)
2c: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIc)
2d: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAId)
2e: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIe)
2f: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIf)
2g: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIg)
2h: 1,4-DIHYDRONICOTINAMIDE ADENINE DI... (NAIh)
3a: OXAMIC ACID (OXMa)
3b: OXAMIC ACID (OXMb)
3c: OXAMIC ACID (OXMc)
3d: OXAMIC ACID (OXMd)
3e: OXAMIC ACID (OXMe)
3f: OXAMIC ACID (OXMf)
3g: OXAMIC ACID (OXMg)
3h: OXAMIC ACID (OXMh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
4
Ligand/Ion
ACETATE ION
2
NAI
4
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3
OXM
4
Ligand/Ion
OXAMIC ACID
[
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Sites
(14, 14)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC2 (SOFTWARE)
06: BC4 (SOFTWARE)
07: BC8 (SOFTWARE)
08: BC9 (SOFTWARE)
09: CC1 (SOFTWARE)
10: CC2 (SOFTWARE)
11: CC3 (SOFTWARE)
12: CC4 (SOFTWARE)
13: CC5 (SOFTWARE)
14: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
ARG E:170 , HIS E:185 , TRP E:187 , HIS G:185
BINDING SITE FOR RESIDUE ACT E 815
02
AC6
SOFTWARE
ARG F:170 , HIS F:185 , HOH F:822 , HOH F:838 , HIS H:185
BINDING SITE FOR RESIDUE ACT F 818
03
AC7
SOFTWARE
LEU E:182 , HIS E:185 , ARG G:170 , HIS G:185 , TRP G:187 , HOH G:822 , HOH G:834
BINDING SITE FOR RESIDUE ACT G 821
04
AC8
SOFTWARE
HIS F:185 , ARG H:170 , HIS H:185
BINDING SITE FOR RESIDUE ACT H 824
05
BC2
SOFTWARE
GLY B:28 , ALA B:29 , VAL B:30 , ASP B:51 , VAL B:52 , ILE B:53 , LYS B:56 , THR B:94 , ALA B:95 , GLY B:96 , ALA B:97 , ARG B:98 , ILE B:115 , ILE B:119 , VAL B:135 , SER B:136 , ASN B:137 , SER B:160 , LEU B:164 , HIS B:192 , THR B:247 , ILE B:251 , OXM B:805 , HOH B:812 , HOH B:814 , HOH B:831 , HOH B:855 , HOH B:907 , HOH B:916 , HOH B:929 , ASN F:107
BINDING SITE FOR RESIDUE NAI B 804
06
BC4
SOFTWARE
GLY C:28 , ALA C:29 , VAL C:30 , ASP C:51 , VAL C:52 , ILE C:53 , LYS C:56 , THR C:94 , ALA C:95 , GLY C:96 , ALA C:97 , ARG C:98 , ILE C:119 , VAL C:135 , ASN C:137 , SER C:160 , LEU C:164 , HIS C:192 , THR C:247 , ILE C:251 , OXM C:808 , HOH C:836 , HOH C:855 , HOH C:856 , HOH C:857 , HOH C:861 , ASN H:107
BINDING SITE FOR RESIDUE NAI C 807
07
BC8
SOFTWARE
GLN A:110 , HOH A:937 , GLY E:28 , ALA E:29 , VAL E:30 , ASP E:51 , VAL E:52 , THR E:94 , ALA E:95 , GLY E:96 , VAL E:135 , ASN E:137 , SER E:160 , LEU E:164 , HIS E:192 , THR E:247 , ILE E:251 , OXM E:814 , HOH E:839 , HOH E:847 , HOH E:851
BINDING SITE FOR RESIDUE NAI E 813
08
BC9
SOFTWARE
ASN E:137 , LEU E:164 , ARG E:168 , HIS E:192 , ALA E:237 , THR E:247 , NAI E:813
BINDING SITE FOR RESIDUE OXM E 814
09
CC1
SOFTWARE
GLY F:28 , ALA F:29 , VAL F:30 , ASP F:51 , VAL F:52 , ILE F:53 , THR F:94 , ALA F:95 , GLY F:96 , ALA F:97 , ARG F:98 , ILE F:115 , VAL F:135 , ASN F:137 , SER F:160 , LEU F:164 , HIS F:192 , THR F:247 , ILE F:251 , OXM F:817 , HOH F:832 , HOH F:837 , HOH F:845 , HOH F:851 , HOH F:861 , HOH F:862
BINDING SITE FOR RESIDUE NAI F 816
10
CC2
SOFTWARE
GLN F:99 , ARG F:105 , ASN F:137 , ARG F:168 , HIS F:192 , ALA F:237 , THR F:247 , NAI F:816
BINDING SITE FOR RESIDUE OXM F 817
11
CC3
SOFTWARE
GLN D:330 , GLY G:28 , ALA G:29 , VAL G:30 , ASP G:51 , VAL G:52 , ILE G:53 , THR G:94 , ALA G:95 , GLY G:96 , VAL G:135 , SER G:136 , ASN G:137 , LEU G:164 , HIS G:192 , THR G:247 , ILE G:251 , OXM G:820 , HOH G:825 , HOH G:831
BINDING SITE FOR RESIDUE NAI G 819
12
CC4
SOFTWARE
ASN G:137 , LEU G:164 , ARG G:168 , HIS G:192 , ALA G:237 , NAI G:819
BINDING SITE FOR RESIDUE OXM G 820
13
CC5
SOFTWARE
GLY H:28 , ALA H:29 , VAL H:30 , ASP H:51 , ILE H:53 , THR H:94 , ALA H:95 , GLY H:96 , ALA H:97 , ARG H:98 , ILE H:115 , VAL H:135 , ASN H:137 , SER H:160 , LEU H:164 , HIS H:192 , THR H:247 , ILE H:251 , OXM H:823 , HOH H:830 , HOH H:847 , HOH H:864 , HOH H:873
BINDING SITE FOR RESIDUE NAI H 822
14
CC6
SOFTWARE
GLN H:99 , ARG H:105 , ASN H:137 , ARG H:168 , HIS H:192 , ALA H:237 , THR H:247 , NAI H:822
BINDING SITE FOR RESIDUE OXM H 823
[
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]
SAPs(SNPs)/Variants
(3, 12)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_059374 (S160R, chain E/F/G/H, )
2: VAR_004180 (K221E, chain E/F/G/H, )
3: VAR_004181 (R314C, chain E/F/G/H, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_059374
S
161
R
LDHA_HUMAN
Polymorphism
5030621
E/F/G/H
S
160
R
2
UniProt
VAR_004180
K
222
E
LDHA_HUMAN
Polymorphism
---
E/F/G/H
K
221
E
3
UniProt
VAR_004181
R
315
C
LDHA_HUMAN
Polymorphism
---
E/F/G/H
R
314
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: L_LDH (E:189-195,F:189-195,G:189-195,H:18...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
L_LDH
PS00064
L-lactate dehydrogenase active site.
LDHA_HUMAN
190-196
4
-
-
-
-
E:189-195
F:189-195
G:189-195
H:189-195
[
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Exons
(0, 0)
Info
All Exons
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d1i10a2 (A:160-331)
1b: SCOP_d1i10c2 (C:160-331)
1c: SCOP_d1i10d2 (D:160-331)
1d: SCOP_d1i10e2 (E:160-331)
1e: SCOP_d1i10f2 (F:160-331)
1f: SCOP_d1i10g2 (G:160-331)
1g: SCOP_d1i10h2 (H:160-331)
1h: SCOP_d1i10b2 (B:160-331)
2a: SCOP_d1i10a1 (A:1-159)
2b: SCOP_d1i10c1 (C:1-159)
2c: SCOP_d1i10d1 (D:1-159)
2d: SCOP_d1i10e1 (E:1-159)
2e: SCOP_d1i10f1 (F:1-159)
2f: SCOP_d1i10g1 (G:1-159)
2g: SCOP_d1i10h1 (H:1-159)
2h: SCOP_d1i10b1 (B:1-159)
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Classes
(
)
(
)
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(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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)
Human (Homo sapiens), muscle isoform (M chain) [TaxId: 9606]
(3)
1a
d1i10a2
A:160-331
1b
d1i10c2
C:160-331
1c
d1i10d2
D:160-331
1d
d1i10e2
E:160-331
1e
d1i10f2
F:160-331
1f
d1i10g2
G:160-331
1g
d1i10h2
H:160-331
1h
d1i10b2
B:160-331
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
:
LDH N-terminal domain-like
(117)
Protein domain
:
Lactate dehydrogenase
(53)
Human (Homo sapiens), muscle isoform (M chain) [TaxId: 9606]
(3)
2a
d1i10a1
A:1-159
2b
d1i10c1
C:1-159
2c
d1i10d1
D:1-159
2d
d1i10e1
E:1-159
2e
d1i10f1
F:1-159
2f
d1i10g1
G:1-159
2g
d1i10h1
H:1-159
2h
d1i10b1
B:1-159
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1i10A01 (A:14-161)
1b: CATH_1i10B01 (B:14-161)
1c: CATH_1i10C01 (C:14-161)
1d: CATH_1i10D01 (D:14-161)
1e: CATH_1i10E01 (E:14-161)
1f: CATH_1i10F01 (F:14-161)
1g: CATH_1i10H01 (H:14-161)
1h: CATH_1i10G01 (G:14-161)
2a: CATH_1i10A02 (A:162-329)
2b: CATH_1i10B02 (B:162-329)
2c: CATH_1i10C02 (C:162-329)
2d: CATH_1i10D02 (D:162-329)
2e: CATH_1i10E02 (E:162-329)
2f: CATH_1i10F02 (F:162-329)
2g: CATH_1i10G02 (G:162-329)
2h: CATH_1i10H02 (H:162-329)
View:
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Classes
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)
(
)
Architectures
(
)
(
)
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)
Human (Homo sapiens)
(188)
1a
1i10A01
A:14-161
1b
1i10B01
B:14-161
1c
1i10C01
C:14-161
1d
1i10D01
D:14-161
1e
1i10E01
E:14-161
1f
1i10F01
F:14-161
1g
1i10H01
H:14-161
1h
1i10G01
G:14-161
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)
Human (Homo sapiens)
(4)
2a
1i10A02
A:162-329
2b
1i10B02
B:162-329
2c
1i10C02
C:162-329
2d
1i10D02
D:162-329
2e
1i10E02
E:162-329
2f
1i10F02
F:162-329
2g
1i10G02
G:162-329
2h
1i10H02
H:162-329
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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