4OKN

Crystal structure of human muscle L-lactate dehydrogenase, ternary complex with NADH and oxalate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0004457	molecular_function	lactate dehydrogenase activity
A	0004459	molecular_function	L-lactate dehydrogenase (NAD+) activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005829	cellular_component	cytosol
A	0006089	biological_process	lactate metabolic process
A	0006096	biological_process	glycolytic process
A	0016020	cellular_component	membrane
A	0016491	molecular_function	oxidoreductase activity
A	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A	0019752	biological_process	carboxylic acid metabolic process
A	0035686	cellular_component	sperm fibrous sheath
A	0042802	molecular_function	identical protein binding
A	0042867	biological_process	pyruvate catabolic process
A	0045296	molecular_function	cadherin binding
A	0070062	cellular_component	extracellular exosome
B	0003824	molecular_function	catalytic activity
B	0004457	molecular_function	lactate dehydrogenase activity
B	0004459	molecular_function	L-lactate dehydrogenase (NAD+) activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005829	cellular_component	cytosol
B	0006089	biological_process	lactate metabolic process
B	0006096	biological_process	glycolytic process
B	0016020	cellular_component	membrane
B	0016491	molecular_function	oxidoreductase activity
B	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B	0019752	biological_process	carboxylic acid metabolic process
B	0035686	cellular_component	sperm fibrous sheath
B	0042802	molecular_function	identical protein binding
B	0042867	biological_process	pyruvate catabolic process
B	0045296	molecular_function	cadherin binding
B	0070062	cellular_component	extracellular exosome
C	0003824	molecular_function	catalytic activity
C	0004457	molecular_function	lactate dehydrogenase activity
C	0004459	molecular_function	L-lactate dehydrogenase (NAD+) activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005829	cellular_component	cytosol
C	0006089	biological_process	lactate metabolic process
C	0006096	biological_process	glycolytic process
C	0016020	cellular_component	membrane
C	0016491	molecular_function	oxidoreductase activity
C	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
C	0019752	biological_process	carboxylic acid metabolic process
C	0035686	cellular_component	sperm fibrous sheath
C	0042802	molecular_function	identical protein binding
C	0042867	biological_process	pyruvate catabolic process
C	0045296	molecular_function	cadherin binding
C	0070062	cellular_component	extracellular exosome
D	0003824	molecular_function	catalytic activity
D	0004457	molecular_function	lactate dehydrogenase activity
D	0004459	molecular_function	L-lactate dehydrogenase (NAD+) activity
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0005829	cellular_component	cytosol
D	0006089	biological_process	lactate metabolic process
D	0006096	biological_process	glycolytic process
D	0016020	cellular_component	membrane
D	0016491	molecular_function	oxidoreductase activity
D	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
D	0019752	biological_process	carboxylic acid metabolic process
D	0035686	cellular_component	sperm fibrous sheath
D	0042802	molecular_function	identical protein binding
D	0042867	biological_process	pyruvate catabolic process
D	0045296	molecular_function	cadherin binding
D	0070062	cellular_component	extracellular exosome
E	0003824	molecular_function	catalytic activity
E	0004457	molecular_function	lactate dehydrogenase activity
E	0004459	molecular_function	L-lactate dehydrogenase (NAD+) activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0005739	cellular_component	mitochondrion
E	0005829	cellular_component	cytosol
E	0006089	biological_process	lactate metabolic process
E	0006096	biological_process	glycolytic process
E	0016020	cellular_component	membrane
E	0016491	molecular_function	oxidoreductase activity
E	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
E	0019752	biological_process	carboxylic acid metabolic process
E	0035686	cellular_component	sperm fibrous sheath
E	0042802	molecular_function	identical protein binding
E	0042867	biological_process	pyruvate catabolic process
E	0045296	molecular_function	cadherin binding
E	0070062	cellular_component	extracellular exosome
F	0003824	molecular_function	catalytic activity
F	0004457	molecular_function	lactate dehydrogenase activity
F	0004459	molecular_function	L-lactate dehydrogenase (NAD+) activity
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005737	cellular_component	cytoplasm
F	0005739	cellular_component	mitochondrion
F	0005829	cellular_component	cytosol
F	0006089	biological_process	lactate metabolic process
F	0006096	biological_process	glycolytic process
F	0016020	cellular_component	membrane
F	0016491	molecular_function	oxidoreductase activity
F	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
F	0019752	biological_process	carboxylic acid metabolic process
F	0035686	cellular_component	sperm fibrous sheath
F	0042802	molecular_function	identical protein binding
F	0042867	biological_process	pyruvate catabolic process
F	0045296	molecular_function	cadherin binding
F	0070062	cellular_component	extracellular exosome
G	0003824	molecular_function	catalytic activity
G	0004457	molecular_function	lactate dehydrogenase activity
G	0004459	molecular_function	L-lactate dehydrogenase (NAD+) activity
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005737	cellular_component	cytoplasm
G	0005739	cellular_component	mitochondrion
G	0005829	cellular_component	cytosol
G	0006089	biological_process	lactate metabolic process
G	0006096	biological_process	glycolytic process
G	0016020	cellular_component	membrane
G	0016491	molecular_function	oxidoreductase activity
G	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
G	0019752	biological_process	carboxylic acid metabolic process
G	0035686	cellular_component	sperm fibrous sheath
G	0042802	molecular_function	identical protein binding
G	0042867	biological_process	pyruvate catabolic process
G	0045296	molecular_function	cadherin binding
G	0070062	cellular_component	extracellular exosome
H	0003824	molecular_function	catalytic activity
H	0004457	molecular_function	lactate dehydrogenase activity
H	0004459	molecular_function	L-lactate dehydrogenase (NAD+) activity
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005737	cellular_component	cytoplasm
H	0005739	cellular_component	mitochondrion
H	0005829	cellular_component	cytosol
H	0006089	biological_process	lactate metabolic process
H	0006096	biological_process	glycolytic process
H	0016020	cellular_component	membrane
H	0016491	molecular_function	oxidoreductase activity
H	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
H	0019752	biological_process	carboxylic acid metabolic process
H	0035686	cellular_component	sperm fibrous sheath
H	0042802	molecular_function	identical protein binding
H	0042867	biological_process	pyruvate catabolic process
H	0045296	molecular_function	cadherin binding
H	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	28
Details	BINDING SITE FOR RESIDUE NAI A 401

Chain	Residue
A	GLY29
A	ALA98
A	ARG99
A	GLN100
A	PHE119
A	ILE120
A	VAL136
A	ASN138
A	SER161
A	HIS193
A	THR248
A	ALA30
A	ILE252
A	OXL402
A	HOH502
A	HOH540
A	HOH556
A	HOH561
A	HOH584
A	HOH585
G	ASN108
A	VAL31
A	ASP52
A	VAL53
A	ILE54
A	THR95
A	ALA96
A	GLY97

---

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE OXL A 402

Chain	Residue
A	GLN100
A	ARG106
A	ASN138
A	ARG169
A	HIS193
A	ALA238
A	THR248
A	NAI401
A	HOH556

---

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 403

Chain	Residue
A	ASN164
A	SER167
A	ARG171
A	PRO272
B	LEU70

---

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE OXL B 401

Chain	Residue
B	ASN138
B	ARG169
B	HIS193
B	THR248
B	HOH592

---

site_id	AC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 B 402

Chain	Residue
B	ARG171
B	HIS186
B	HOH516
B	HOH519
B	HOH541
B	HOH546
D	LEU183
D	HIS186

---

site_id	AC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE KAN B 403

Chain	Residue
B	ASP52
B	VAL53
B	ALA96
B	GLY97
B	ARG99
B	ARG112
B	ILE116
B	PHE119
B	ILE120
H	GLU55
H	HOH556

---

site_id	AC7
Number of Residues	30
Details	BINDING SITE FOR RESIDUE NAI C 401

Chain	Residue
C	GLY29
C	ALA30
C	VAL31
C	ASP52
C	VAL53
C	ILE54
C	LYS57
C	THR95
C	ALA96
C	GLY97
C	ALA98
C	ARG99
C	ASN113
C	ILE120
C	VAL136
C	ASN138
C	SER161
C	HIS193
C	THR248
C	ILE252
C	OXL402
C	HOH503
C	HOH509
C	HOH525
C	HOH528
C	HOH544
C	HOH575
C	HOH579
C	HOH593
C	HOH604

---

site_id	AC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE OXL C 402

Chain	Residue
C	LEU165
C	ARG169
C	HIS193
C	ALA238
C	THR248
C	NAI401
C	HOH544
C	GLN100
C	ARG106
C	ASN138

---

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 C 403

Chain	Residue
C	ASN164
C	SER167
C	ARG171
C	PRO272
D	LEU70

---

site_id	BC1
Number of Residues	34
Details	BINDING SITE FOR RESIDUE NAI D 401

Chain	Residue
D	GLY29
D	ALA30
D	VAL31
D	ASP52
D	VAL53
D	ILE54
D	LYS57
D	THR95
D	ALA96
D	GLY97
D	ALA98
D	ARG99
D	GLN100
D	ASN113
D	ILE116
D	ILE120
D	VAL136
D	ASN138
D	SER161
D	LEU165
D	HIS193
D	THR248
D	ILE252
D	OXL402
D	HOH501
D	HOH525
D	HOH550
D	HOH563
D	HOH589
D	HOH590
D	HOH593
D	HOH629
E	GLY103
E	ASN108

---

site_id	BC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE OXL D 402

Chain	Residue
D	GLN100
D	ARG106
D	ASN138
D	ARG169
D	HIS193
D	ALA238
D	THR248
D	NAI401
D	HOH589

---

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 D 403

Chain	Residue
C	LEU70
D	ASN164
D	SER167
D	ARG171
D	PRO272
D	HOH596

---

site_id	BC4
Number of Residues	30
Details	BINDING SITE FOR RESIDUE NAI E 401

Chain	Residue
E	GLY29
E	ALA30
E	VAL31
E	ASP52
E	VAL53
E	ILE54
E	LYS57
E	THR95
E	ALA96
E	GLY97
E	ALA98
E	ARG99
E	GLN100
E	ASN113
E	ILE116
E	ILE120
E	VAL136
E	ASN138
E	SER161
E	LEU165
E	HIS193
E	THR248
E	ILE252
E	OXL402
E	HOH504
E	HOH509
E	HOH514
E	HOH547
E	HOH571
E	HOH575

---

site_id	BC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE OXL E 402

Chain	Residue
E	GLN100
E	ARG106
E	ASN138
E	ARG169
E	HIS193
E	ALA238
E	THR248
E	NAI401
E	HOH514

---

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 E 403

Chain	Residue
E	ASN164
E	SER167
E	ARG171
E	PRO272

---

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 E 404

Chain	Residue
D	GLY97
D	ALA98
D	ILE116
D	HOH563
D	HOH578
E	ASN108

---

site_id	BC8
Number of Residues	28
Details	BINDING SITE FOR RESIDUE NAI F 401

Chain	Residue
C	GLN111
F	GLY29
F	ALA30
F	VAL31
F	ASP52
F	VAL53
F	ILE54
F	LYS57
F	THR95
F	ALA96
F	GLY97
F	ALA98
F	ARG99
F	ILE116
F	VAL136
F	ASN138
F	SER161
F	HIS193
F	THR248
F	ILE252
F	OXL402
F	HOH501
F	HOH503
F	HOH544
F	HOH566
F	HOH567
F	HOH589
F	HOH596

---

site_id	BC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE OXL F 402

Chain	Residue
F	GLN100
F	ARG106
F	ASN138
F	ARG169
F	HIS193
F	ALA238
F	THR248
F	NAI401
F	HOH596

---

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 F 403

Chain	Residue
E	LEU70
F	ASN164
F	SER167
F	ARG171
F	PRO272

---

site_id	CC2
Number of Residues	27
Details	BINDING SITE FOR RESIDUE NAI G 401

Chain	Residue
G	GLY29
G	ALA30
G	VAL31
G	ASP52
G	VAL53
G	ILE54
G	LYS57
G	THR95
G	ALA96
G	GLY97
G	ALA98
G	ARG99
G	GLN100
G	ILE116
G	VAL136
G	ASN138
G	SER161
G	LEU165
G	HIS193
G	THR248
G	ILE252
G	OXL402
G	HOH502
G	HOH510
G	HOH515
G	HOH530
G	HOH576

---

site_id	CC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE OXL G 402

Chain	Residue
G	GLN100
G	ARG106
G	ASN138
G	ARG169
G	HIS193
G	ALA238
G	THR248
G	NAI401

---

site_id	CC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 G 403

Chain	Residue
G	ASN164
G	SER167
G	ARG171
G	PRO272
H	LEU70

---

site_id	CC5
Number of Residues	26
Details	BINDING SITE FOR RESIDUE NAI H 401

Chain	Residue
H	GLY29
H	ALA30
H	VAL31
H	ASP52
H	ILE54
H	THR95
H	ALA96
H	GLY97
H	ALA98
H	ARG99
H	ILE116
H	PHE119
H	ILE120
H	VAL136
H	ASN138
H	SER161
H	LEU165
H	HIS193
H	THR248
H	ILE252
H	OXL402
H	HOH502
H	HOH507
H	HOH517
H	HOH521
H	HOH550

---

site_id	CC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE OXL H 402

Chain	Residue
H	GLN100
H	ARG106
H	ASN138
H	ARG169
H	HIS193
H	ALA238
H	THR248
H	NAI401

---

site_id	CC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 H 403

Chain	Residue
G	LEU70
H	ASN164
H	SER167
H	ARG171
H	TRP188
H	PRO272

---

Functional Information from PROSITE/UniProt

site_id	PS00064
Number of Residues	7
Details	L_LDH L-lactate dehydrogenase active site. LGEHGDS

Chain	Residue	Details
A	LEU190-SER196

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Active site: {"description":"Proton acceptor"}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	232
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11276087","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	32
Details	Binding site: {}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	8
Details	Modified residue: {"description":"N-acetylalanine","evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2005","submissionDatabase":"UniProtKB","authors":["Bienvenut W.V."]}},{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"22223895","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	24
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P06151","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	8
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	24
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	8
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	8
Details	Modified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	24
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P06151","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	8
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P06151","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	16
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P04642","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	8
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	16
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---