Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5W8J

Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 29

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	17
Details	binding site for residue 9Y7 A 501

Chain	Residue
A	GLN99
A	HIS192
A	GLY193
A	THR247
A	LEU322
A	DMS504
A	HOH642
A	HOH688
A	HOH742
A	LEU108
A	ASN137
A	PRO138
A	VAL139
A	ASP140
A	ILE141
A	ARG168
A	GLU191

site_id	AC2
Number of Residues	16
Details	binding site for residue 9Y7 A 502

Chain	Residue
A	VAL25
A	GLY26
A	VAL50
A	ASP51
A	VAL52
A	LYS80
A	TYR82
A	ALA95
A	GLY96
A	ILE115
A	PHE118
A	ILE119
A	HOH603
A	HOH696
A	HOH701
A	HOH772

site_id	AC3
Number of Residues	10
Details	binding site for residue MLA A 503

Chain	Residue
A	ARG170
A	HIS185
A	VAL269
A	HOH630
A	HOH662
A	HOH681
A	HOH684
A	HOH692
C	SER183
C	HIS185

site_id	AC4
Number of Residues	5
Details	binding site for residue DMS A 504

Chain	Residue
A	TYR238
A	ILE241
A	9Y7501
A	HOH639
A	HOH808

site_id	AC5
Number of Residues	6
Details	binding site for residue DMS A 505

Chain	Residue
A	LEU213
A	HOH640
B	LYS125
B	TYR126
B	HOH604
C	THR306

site_id	AC6
Number of Residues	12
Details	binding site for residue GOL A 506

Chain	Residue
A	SER201
A	GLY202
A	MET203
A	ASN204
A	GLY207
A	SER209
A	HOH736
C	SER201
C	GLY202
C	MET203
C	ASN204
C	SER209

site_id	AC7
Number of Residues	9
Details	binding site for residue MLA B 401

Chain	Residue
B	GLN99
B	ARG105
B	ASN137
B	LEU164
B	ARG168
B	HIS192
B	ALA237
B	THR247
B	HOH623

site_id	AC8
Number of Residues	17
Details	binding site for residue 9Y7 B 402

Chain	Residue
B	VAL25
B	GLY26
B	VAL50
B	ASP51
B	VAL52
B	LYS80
B	TYR82
B	ALA95
B	GLY96
B	ARG98
B	ARG111
B	ILE115
B	ILE119
B	HOH504
B	HOH568
B	HOH573
B	HOH667

site_id	AC9
Number of Residues	11
Details	binding site for residue MLA B 403

Chain	Residue
B	HOH695
D	SER183
D	HIS185
D	HOH602
B	ARG170
B	HIS185
B	ARG268
B	VAL269
B	HOH502
B	HOH511
B	HOH522

site_id	AD1
Number of Residues	11
Details	binding site for residue MLA C 401

Chain	Residue
A	SER183
A	HIS185
C	ARG170
C	HIS185
C	VAL269
C	HOH533
C	HOH538
C	HOH540
C	HOH554
C	HOH566
C	HOH583

site_id	AD2
Number of Residues	18
Details	binding site for residue 9Y7 C 402

Chain	Residue
C	GLN99
C	ARG105
C	LEU108
C	ASN137
C	PRO138
C	VAL139
C	ASP140
C	ILE141
C	ARG168
C	GLU191
C	HIS192
C	THR247
C	LEU322
C	DMS404
C	HOH512
C	HOH557
C	HOH605
C	HOH698

site_id	AD3
Number of Residues	19
Details	binding site for residue 9Y7 C 403

Chain	Residue
C	VAL25
C	GLY26
C	VAL50
C	ASP51
C	VAL52
C	LYS80
C	TYR82
C	ALA95
C	GLY96
C	ALA97
C	ILE115
C	PHE118
C	ILE119
C	HOH507
C	HOH532
C	HOH628
C	HOH638
C	HOH661
D	GLU101

site_id	AD4
Number of Residues	3
Details	binding site for residue DMS C 404

Chain	Residue
C	TYR238
C	ILE241
C	9Y7402

site_id	AD5
Number of Residues	11
Details	binding site for residue MLA D 401

Chain	Residue
B	SER183
B	HIS185
B	HOH551
D	ARG170
D	HIS185
D	VAL269
D	HOH524
D	HOH533
D	HOH576
D	HOH581
D	HOH645

site_id	AD6
Number of Residues	18
Details	binding site for residue 9Y7 D 402

Chain	Residue
D	ARG105
D	LEU108
D	ASN137
D	PRO138
D	VAL139
D	ASP140
D	ILE141
D	ARG168
D	GLU191
D	HIS192
D	THR247
D	LEU322
D	DMS403
D	DMS404
D	HOH545
D	HOH562
D	HOH629
D	HOH642

site_id	AD7
Number of Residues	7
Details	binding site for residue DMS D 403

Chain	Residue
D	GLY96
D	ALA97
D	SER136
D	ASN137
D	9Y7402
D	HOH543
D	HOH686

site_id	AD8
Number of Residues	4
Details	binding site for residue DMS D 404

Chain	Residue
D	TYR238
D	ILE241
D	9Y7402
D	HOH507

site_id	AD9
Number of Residues	10
Details	binding site for residue GOL D 405

Chain	Residue
B	GLY202
B	ASN204
B	GLY207
B	HOH523
D	SER201
D	GLY202
D	MET203
D	ASN204
D	GLY207
D	SER209

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)