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1I10
Asym. Unit
Info
Asym.Unit (445 KB)
Biol.Unit 1 (223 KB)
Biol.Unit 2 (219 KB)
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(1)
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
[
close entry info
]
Hetero Components
(3, 24)
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
8
Ligand/Ion
ACETATE ION
2
NAI
8
Ligand/Ion
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3
OXM
8
Ligand/Ion
OXAMIC ACID
[
close Hetero Component info
]
Sites
(24, 24)
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)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:170 , HIS A:185 , HOH A:898 , HOH A:900 , HOH A:907 , LEU C:182 , HIS C:185
BINDING SITE FOR RESIDUE ACT A 803
02
AC2
SOFTWARE
ARG B:170 , HIS B:185 , HOH B:839 , HOH B:848 , HOH B:891 , HIS D:185
BINDING SITE FOR RESIDUE ACT B 806
03
AC3
SOFTWARE
HIS A:185 , HOH A:895 , HOH A:928 , ARG C:170 , HIS C:185 , HOH C:854
BINDING SITE FOR RESIDUE ACT C 809
04
AC4
SOFTWARE
HIS B:185 , HOH B:816 , ARG D:170 , HIS D:185 , HOH D:825 , HOH D:855
BINDING SITE FOR RESIDUE ACT D 812
05
AC5
SOFTWARE
ARG E:170 , HIS E:185 , TRP E:187 , HIS G:185
BINDING SITE FOR RESIDUE ACT E 815
06
AC6
SOFTWARE
ARG F:170 , HIS F:185 , HOH F:822 , HOH F:838 , HIS H:185
BINDING SITE FOR RESIDUE ACT F 818
07
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
08
AC8
SOFTWARE
HIS F:185 , ARG H:170 , HIS H:185
BINDING SITE FOR RESIDUE ACT H 824
09
AC9
SOFTWARE
GLY A:28 , ALA A:29 , VAL A:30 , ASP A:51 , VAL A:52 , ILE A:53 , LYS A:56 , THR A:94 , ALA A:95 , GLY A:96 , ALA A:97 , ARG A:98 , ILE A:119 , VAL A:135 , ASN A:137 , SER A:160 , LEU A:164 , HIS A:192 , THR A:247 , ILE A:251 , OXM A:802 , HOH A:804 , HOH A:807 , HOH A:814 , HOH A:826 , HOH A:851 , HOH A:864 , HOH A:877 , HOH A:885
BINDING SITE FOR RESIDUE NAI A 801
10
BC1
SOFTWARE
GLN A:99 , ARG A:105 , ASN A:137 , LEU A:164 , ARG A:168 , HIS A:192 , ALA A:237 , THR A:247 , NAI A:801
BINDING SITE FOR RESIDUE OXM A 802
11
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
12
BC3
SOFTWARE
GLN B:99 , ARG B:105 , ASN B:137 , ARG B:168 , HIS B:192 , ALA B:237 , THR B:247 , NAI B:804
BINDING SITE FOR RESIDUE OXM B 805
13
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
14
BC5
SOFTWARE
GLN C:99 , ARG C:105 , ASN C:137 , ARG C:168 , HIS C:192 , ALA C:237 , THR C:247 , NAI C:807
BINDING SITE FOR RESIDUE OXM C 808
15
BC6
SOFTWARE
GLY D:26 , GLY D:28 , ALA D:29 , VAL D:30 , ASP D:51 , VAL D:52 , ILE D:53 , THR D:94 , ALA D:95 , GLY D:96 , ARG D:98 , ILE D:115 , ILE D:119 , VAL D:135 , ASN D:137 , SER D:160 , HIS D:192 , OXM D:811 , HOH D:858 , HOH D:889
BINDING SITE FOR RESIDUE NAI D 810
16
BC7
SOFTWARE
ASN D:137 , ARG D:168 , HIS D:192 , ALA D:237 , THR D:247 , NAI D:810
BINDING SITE FOR RESIDUE OXM D 811
17
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
18
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
19
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
20
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
21
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
22
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
23
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
24
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
[
close Site info
]
SAPs(SNPs)/Variants
(3, 24)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_059374 (S160R, chain A/B/C/D/E/F/G/H, )
2: VAR_004180 (K221E, chain A/B/C/D/E/F/G/H, )
3: VAR_004181 (R314C, chain A/B/C/D/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
A/B/C/D/E/F/G/H
S
160
R
2
UniProt
VAR_004180
K
222
E
LDHA_HUMAN
Polymorphism
---
A/B/C/D/E/F/G/H
K
221
E
3
UniProt
VAR_004181
R
315
C
LDHA_HUMAN
Polymorphism
---
A/B/C/D/E/F/G/H
R
314
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: L_LDH (A:189-195,B:189-195,C:189-195,D: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
8
A:189-195
B:189-195
C:189-195
D:189-195
E:189-195
F:189-195
G:189-195
H:189-195
[
close PROSITE info
]
Exons
(12, 96)
Info
All Exons
Exon 1.3a (A:1-41 | B:1-41 | C:1-41 | D:1-41 ...)
Exon 1.5b (A:42-81 | B:42-81 | C:42-81 | D:42...)
Exon 1.6c (A:81-139 | B:81-139 | C:81-139 | D...)
Exon 1.7 (A:139-197 | B:139-197 | C:139-197 ...)
Exon 1.8c (A:197-231 | B:197-231 | C:197-231 ...)
Exon 1.9 (A:231-232 | B:231-232 | C:231-232 ...)
Exon 1.10 (A:232-250 | B:232-250 | C:232-250 ...)
Exon 1.11 (A:250-253 | B:250-253 | C:250-253 ...)
Exon 1.12 (A:253-262 | B:253-262 | C:253-262 ...)
Exon 1.13 (A:262-271 | B:262-271 | C:262-271 ...)
Exon 1.14b (A:271-276 | B:271-276 | C:271-276 ...)
Exon 1.15a (A:277-330 | B:277-330 | C:277-330 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1f/1.3a
02: Boundary 1.3a/1.5b
03: Boundary 1.5b/1.6c
04: Boundary 1.6c/1.7
05: Boundary 1.7/1.8c
06: Boundary 1.8c/1.9
07: Boundary 1.9/1.10
08: Boundary 1.10/1.11
09: Boundary 1.11/1.12
10: Boundary 1.12/1.13
11: Boundary 1.13/1.14b
12: Boundary 1.14b/1.15a
13: Boundary 1.15a/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1f
ENST00000379412
1f
ENSE00001524368
chr11:
18416112-18416183
72
LDHA_HUMAN
-
0
0
-
-
1.3a
ENST00000379412
3a
ENSE00002196319
chr11:
18418366-18418515
150
LDHA_HUMAN
1-42
42
8
A:1-41
B:1-41
C:1-41
D:1-41
E:1-41
F:1-41
G:1-41
H:1-41
41
41
41
41
41
41
41
41
1.5b
ENST00000379412
5b
ENSE00000886595
chr11:
18420978-18421095
118
LDHA_HUMAN
43-82
40
8
A:42-81
B:42-81
C:42-81
D:42-81
E:42-81
F:42-81
G:42-81
H:42-81
40
40
40
40
40
40
40
40
1.6c
ENST00000379412
6c
ENSE00001106716
chr11:
18422384-18422557
174
LDHA_HUMAN
82-140
59
8
A:81-139
B:81-139
C:81-139
D:81-139
E:81-139
F:81-139
G:81-139 (gaps)
H:81-139
59
59
59
59
59
59
59
59
1.7
ENST00000379412
7
ENSE00001639138
chr11:
18424387-18424560
174
LDHA_HUMAN
140-198
59
8
A:139-197
B:139-197
C:139-197
D:139-197
E:139-197
F:139-197
G:139-197
H:139-197
59
59
59
59
59
59
59
59
1.8c
ENST00000379412
8c
ENSE00001655143
chr11:
18425241-18425343
103
LDHA_HUMAN
198-232
35
8
A:197-231
B:197-231
C:197-231
D:197-231
E:197-231
F:197-231
G:197-231
H:197-231
35
35
35
35
35
35
35
35
1.9
ENST00000379412
9
ENSE00001610496
chr11:
18425416-18425418
3
LDHA_HUMAN
232-233
2
8
A:231-232
B:231-232
C:231-232
D:231-232
E:231-232
F:231-232
G:231-232
H:231-232
2
2
2
2
2
2
2
2
1.10
ENST00000379412
10
ENSE00001721839
chr11:
18426327-18426380
54
LDHA_HUMAN
233-251
19
8
A:232-250
B:232-250
C:232-250
D:232-250
E:232-250
F:232-250
G:232-250
H:232-250
19
19
19
19
19
19
19
19
1.11
ENST00000379412
11
ENSE00001697756
chr11:
18426430-18426437
8
LDHA_HUMAN
251-254
4
8
A:250-253
B:250-253
C:250-253
D:250-253
E:250-253
F:250-253
G:250-253
H:250-253
4
4
4
4
4
4
4
4
1.12
ENST00000379412
12
ENSE00001605016
chr11:
18426514-18426540
27
LDHA_HUMAN
254-263
10
8
A:253-262
B:253-262
C:253-262
D:253-262
E:253-262
F:253-262
G:253-262
H:253-262
10
10
10
10
10
10
10
10
1.13
ENST00000379412
13
ENSE00001770181
chr11:
18426715-18426741
27
LDHA_HUMAN
263-272
10
8
A:262-271
B:262-271
C:262-271
D:262-271
E:262-271
F:262-271
G:262-271
H:262-271
10
10
10
10
10
10
10
10
1.14b
ENST00000379412
14b
ENSE00001654863
chr11:
18427103-18427119
17
LDHA_HUMAN
272-277
6
8
A:271-276
B:271-276
C:271-276
D:271-276
E:271-276
F:271-276
G:271-276
H:271-276
6
6
6
6
6
6
6
6
1.15a
ENST00000379412
15a
ENSE00001681791
chr11:
18428664-18429393
730
LDHA_HUMAN
278-331
54
8
A:277-330
B:277-330
C:277-330
D:277-330
E:277-330
F:277-330
G:277-330
H:277-330
54
54
54
54
54
54
54
54
[
close EXON info
]
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)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
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)
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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)
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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