Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5W8L

Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 59 and NADH

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	36
Details	binding site for residue NAI A 401

Chain	Residue
A	GLY28
A	ARG98
A	ILE115
A	ILE119
A	VAL135
A	SER136
A	ASN137
A	SER160
A	LEU164
A	HIS192
A	THR247
A	ALA29
A	ILE251
A	9YA402
A	HOH517
A	HOH523
A	HOH533
A	HOH556
A	HOH558
A	HOH564
A	HOH575
A	HOH588
A	VAL30
A	HOH607
A	HOH614
A	HOH652
A	HOH656
A	HOH664
A	HOH674
A	HOH719
A	ASP51
A	VAL52
A	ILE53
A	THR94
A	ALA95
A	GLY96

site_id	AC2
Number of Residues	21
Details	binding site for residue 9YA A 402

Chain	Residue
A	ARG105
A	VAL109
A	ASN137
A	PRO138
A	VAL139
A	ASP140
A	ILE141
A	LEU164
A	ARG168
A	GLU191
A	HIS192
A	ASP194
A	ALA237
A	TYR238
A	THR247
A	LEU322
A	NAI401
A	EDO404
A	EDO405
A	HOH754
D	GLU328

site_id	AC3
Number of Residues	6
Details	binding site for residue EDO A 403

Chain	Residue
A	LEU11
A	LEU12
A	LYS13
B	LYS125
B	TYR126
B	HOH664

site_id	AC4
Number of Residues	4
Details	binding site for residue EDO A 404

Chain	Residue
A	ARG105
A	ILE241
A	9YA402
A	HOH675

site_id	AC5
Number of Residues	5
Details	binding site for residue EDO A 405

Chain	Residue
A	GLU191
A	THR321
A	LEU322
A	9YA402
D	GLY324

site_id	AC6
Number of Residues	3
Details	binding site for residue EDO A 406

Chain	Residue
A	TYR280
A	LYS304
A	VAL305

site_id	AC7
Number of Residues	33
Details	binding site for residue NAI B 401

Chain	Residue
B	HOH555
B	HOH566
B	HOH584
B	HOH585
B	HOH615
B	HOH632
B	HOH634
B	HOH673
B	HOH711
B	GLY28
B	ALA29
B	VAL30
B	ASP51
B	VAL52
B	ILE53
B	THR94
B	ALA95
B	GLY96
B	ARG98
B	ILE115
B	VAL135
B	SER136
B	ASN137
B	SER160
B	LEU164
B	HIS192
B	THR247
B	ILE251
B	9YA402
B	HOH505
B	HOH524
B	HOH529
B	HOH550

site_id	AC8
Number of Residues	20
Details	binding site for residue 9YA B 402

Chain	Residue
B	ARG105
B	LEU108
B	ASN137
B	PRO138
B	VAL139
B	ASP140
B	ILE141
B	ARG168
B	GLU191
B	HIS192
B	ASP194
B	ALA237
B	TYR238
B	ILE241
B	THR247
B	LEU322
B	NAI401
B	EDO403
B	HOH684
B	HOH766

site_id	AC9
Number of Residues	5
Details	binding site for residue EDO B 403

Chain	Residue
B	ARG105
B	TYR238
B	ILE241
B	9YA402
B	HOH543

site_id	AD1
Number of Residues	34
Details	binding site for residue NAI C 401

Chain	Residue
C	GLY28
C	ALA29
C	VAL30
C	ASP51
C	VAL52
C	ILE53
C	THR94
C	ALA95
C	GLY96
C	ARG98
C	ILE115
C	ILE119
C	VAL135
C	SER136
C	ASN137
C	SER160
C	LEU164
C	HIS192
C	THR247
C	ILE251
C	9YA402
C	HOH502
C	HOH518
C	HOH532
C	HOH550
C	HOH576
C	HOH604
C	HOH613
C	HOH614
C	HOH618
C	HOH643
C	HOH650
C	HOH654
C	HOH678

site_id	AD2
Number of Residues	18
Details	binding site for residue 9YA C 402

Chain	Residue
C	ARG105
C	ASN137
C	PRO138
C	VAL139
C	ASP140
C	ILE141
C	LEU164
C	ARG168
C	GLU191
C	HIS192
C	ASP194
C	ALA237
C	TYR238
C	THR247
C	LEU322
C	NAI401
C	HOH657
C	HOH741

site_id	AD3
Number of Residues	4
Details	binding site for residue EDO C 403

Chain	Residue
C	ARG105
C	ILE241
C	EDO404
C	HOH624

site_id	AD4
Number of Residues	5
Details	binding site for residue EDO C 404

Chain	Residue
C	TYR238
C	ILE241
C	EDO403
C	HOH513
C	HOH587

site_id	AD5
Number of Residues	4
Details	binding site for residue EDO C 405

Chain	Residue
C	ARG176
C	GLU228
C	VAL229
C	HOH552

site_id	AD6
Number of Residues	7
Details	binding site for residue EDO C 406

Chain	Residue
A	LEU69
A	HOH714
C	ASN163
C	ARG170
C	PRO271
C	HOH554
C	HOH560

site_id	AD7
Number of Residues	34
Details	binding site for residue NAI D 401

Chain	Residue
D	GLY28
D	ALA29
D	VAL30
D	ASP51
D	VAL52
D	ILE53
D	THR94
D	ALA95
D	GLY96
D	ARG98
D	ILE115
D	ILE119
D	VAL135
D	SER136
D	ASN137
D	SER160
D	LEU164
D	HIS192
D	THR247
D	ILE251
D	9YA402
D	HOH508
D	HOH518
D	HOH520
D	HOH540
D	HOH551
D	HOH553
D	HOH563
D	HOH572
D	HOH585
D	HOH593
D	HOH598
D	HOH626
D	HOH641

site_id	AD8
Number of Residues	19
Details	binding site for residue 9YA D 402

Chain	Residue
A	GLU328
D	ARG105
D	ASN137
D	PRO138
D	VAL139
D	ASP140
D	ILE141
D	ARG168
D	GLU191
D	HIS192
D	ASP194
D	ALA237
D	TYR238
D	ILE241
D	THR247
D	LEU322
D	NAI401
D	EDO403
D	EDO406

site_id	AD9
Number of Residues	4
Details	binding site for residue EDO D 403

Chain	Residue
D	ARG105
D	ILE241
D	9YA402
D	HOH675

site_id	AE1
Number of Residues	4
Details	binding site for residue EDO D 404

Chain	Residue
D	ARG176
D	GLU228
D	VAL229
D	HOH544

site_id	AE2
Number of Residues	5
Details	binding site for residue EDO D 405

Chain	Residue
A	TRP323
D	SER195
D	ARG314
D	HOH552
D	HOH672

site_id	AE3
Number of Residues	6
Details	binding site for residue EDO D 406

Chain	Residue
A	GLY324
D	GLU191
D	THR321
D	LEU322
D	ILE325
D	9YA402

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	LEU189-SER195

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Proton acceptor"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	116
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11276087","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	16
Details	Binding site: {}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
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	12
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	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	12
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	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
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	12
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	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P06151","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	8
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P04642","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	4
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	8
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

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)