Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5W8I

Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 23 and Zinc

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	3
Details	binding site for residue ZN A 401

Chain	Residue
A	HIS192
A	9YD403
A	HOH684

site_id	AC2
Number of Residues	2
Details	binding site for residue ZN A 402

Chain	Residue
A	CIT404
C	CIT403

site_id	AC3
Number of Residues	9
Details	binding site for residue 9YD A 403

Chain	Residue
A	ARG168
A	HIS192
A	THR247
A	ZN401
A	HOH567
A	GLN99
A	ARG105
A	LEU108
A	ASN137

site_id	AC4
Number of Residues	15
Details	binding site for residue CIT A 404

Chain	Residue
A	ARG170
A	LEU182
A	ARG268
A	VAL269
A	ZN402
A	HOH509
A	HOH511
A	HOH534
A	HOH626
A	HOH651
C	LEU182
C	SER183
C	HIS185
C	CIT403
C	HOH553

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

Chain	Residue
A	ASN163
A	SER166
A	ARG170
A	HOH506
B	LEU69

site_id	AC6
Number of Residues	8
Details	binding site for residue MLA B 401

Chain	Residue
B	ARG105
B	ASN137
B	LEU164
B	ARG168
B	HIS192
B	ALA237
B	THR247
B	HOH568

site_id	AC7
Number of Residues	14
Details	binding site for residue CIT B 402

Chain	Residue
B	ARG170
B	LEU182
B	ARG268
B	VAL269
B	HOH532
B	HOH600
B	HOH659
C	HOH502
D	LEU182
D	SER183
D	HIS185
D	ZN401
D	CIT404
D	HOH503

site_id	AC8
Number of Residues	5
Details	binding site for residue DMS B 403

Chain	Residue
A	LEU69
B	ASN163
B	SER166
B	ARG170
B	HOH503

site_id	AC9
Number of Residues	9
Details	binding site for residue GOL B 404

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

site_id	AD1
Number of Residues	3
Details	binding site for residue ZN C 401

Chain	Residue
C	HIS192
C	9YD402
C	HOH668

site_id	AD2
Number of Residues	10
Details	binding site for residue 9YD C 402

Chain	Residue
C	GLN99
C	ARG105
C	LEU108
C	ASN137
C	ARG168
C	HIS192
C	THR247
C	ZN401
C	HOH597
C	HOH668

site_id	AD3
Number of Residues	15
Details	binding site for residue CIT C 403

Chain	Residue
A	LEU182
A	SER183
A	HIS185
A	ZN402
A	CIT404
A	HOH509
A	HOH524
B	HOH511
C	ARG170
C	LEU182
C	ARG268
C	VAL269
C	HOH520
C	HOH610
C	HOH653

site_id	AD4
Number of Residues	4
Details	binding site for residue DMS C 404

Chain	Residue
C	SER166
C	ARG170
C	HOH507
C	ASN163

site_id	AD5
Number of Residues	2
Details	binding site for residue ZN D 401

Chain	Residue
B	CIT402
D	CIT404

site_id	AD6
Number of Residues	3
Details	binding site for residue ZN D 402

Chain	Residue
D	HIS192
D	9YD403
D	HOH687

site_id	AD7
Number of Residues	10
Details	binding site for residue 9YD D 403

Chain	Residue
D	GLN99
D	LEU108
D	ASN137
D	ARG168
D	HIS192
D	ALA237
D	THR247
D	ZN402
D	HOH611
D	HOH640

site_id	AD8
Number of Residues	15
Details	binding site for residue CIT D 404

Chain	Residue
B	LEU182
B	SER183
B	HIS185
B	CIT402
D	ARG170
D	LEU182
D	ARG268
D	VAL269
D	ZN401
D	HOH503
D	HOH504
D	HOH531
D	HOH538
D	HOH620
D	HOH660

site_id	AD9
Number of Residues	5
Details	binding site for residue DMS D 405

Chain	Residue
C	LEU69
D	ASN163
D	SER166
D	ARG170
D	HOH505

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)