Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5W8K

Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 29 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	14
Details	binding site for residue 9Y7 A 501

Chain	Residue
A	VAL109
A	THR247
A	LEU322
A	NAI502
A	HOH609
A	HOH631
A	ASN137
A	PRO138
A	VAL139
A	ASP140
A	ILE141
A	ARG168
A	GLU191
A	HIS192

site_id	AC2
Number of Residues	30
Details	binding site for residue NAI A 502

Chain	Residue
A	GLY28
A	ALA29
A	VAL30
A	ASP51
A	VAL52
A	ILE53
A	LYS56
A	THR94
A	ALA95
A	GLY96
A	ALA97
A	ARG98
A	ILE115
A	VAL135
A	SER136
A	ASN137
A	SER160
A	LEU164
A	HIS192
A	THR247
A	ILE251
A	9Y7501
A	HOH609
A	HOH612
A	HOH652
A	HOH660
A	HOH661
A	HOH693
A	HOH740
A	HOH744

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

Chain	Residue
A	ARG170
A	HIS185
A	VAL269
A	HOH626
A	HOH634
A	HOH647
A	HOH674
A	HOH720
C	SER183
C	HIS185

site_id	AC4
Number of Residues	12
Details	binding site for residue GOL A 504

Chain	Residue
A	SER201
A	GLY202
A	MET203
A	ASN204
A	SER209
A	HOH615
C	SER201
C	GLY202
C	MET203
C	ASN204
C	SER209
C	GOL504

site_id	AC5
Number of Residues	5
Details	binding site for residue GOL A 505

Chain	Residue
A	LEU279
A	TYR280
A	VAL305
A	HOH642
A	HOH742

site_id	AC6
Number of Residues	7
Details	binding site for residue GOL A 506

Chain	Residue
A	TYR171
A	GLU175
A	HOH714
A	HOH772
A	HOH806
B	MET62
B	GLN65

site_id	AC7
Number of Residues	6
Details	binding site for residue GOL A 507

Chain	Residue
A	MET40
A	ASP42
A	HOH610
A	HOH682
A	HOH702
B	MET40

site_id	AC8
Number of Residues	6
Details	binding site for residue GOL A 508

Chain	Residue
A	GLY281
A	ILE282
A	LYS283
A	ASP284
A	ALA319
A	ASP320

site_id	AC9
Number of Residues	9
Details	binding site for residue MLA B 401

Chain	Residue
B	GLN99
B	ARG105
B	ASN137
B	ARG168
B	HIS192
B	ALA237
B	THR247
B	NAI402
B	HOH553

site_id	AD1
Number of Residues	32
Details	binding site for residue NAI B 402

Chain	Residue
B	GLY28
B	ALA29
B	VAL30
B	ASP51
B	VAL52
B	ILE53
B	LYS56
B	THR94
B	ALA95
B	GLY96
B	ALA97
B	ARG98
B	ILE115
B	VAL135
B	ASN137
B	SER160
B	LEU164
B	HIS192
B	THR247
B	ILE251
B	MLA401
B	HOH520
B	HOH534
B	HOH542
B	HOH546
B	HOH553
B	HOH571
B	HOH586
B	HOH628
B	HOH633
B	HOH638
B	HOH706

site_id	AD2
Number of Residues	11
Details	binding site for residue MLA B 403

Chain	Residue
B	ARG170
B	HIS185
B	VAL269
B	GOL406
B	HOH505
B	HOH529
B	HOH558
B	HOH642
B	HOH664
D	SER183
D	HIS185

site_id	AD3
Number of Residues	4
Details	binding site for residue GOL B 404

Chain	Residue
B	LEU279
B	TYR280
B	VAL305
B	HOH647

site_id	AD4
Number of Residues	7
Details	binding site for residue GOL B 405

Chain	Residue
B	GLY207
B	SER209
B	HOH533
B	HOH549
B	HOH587
D	SER201
D	GOL504

site_id	AD5
Number of Residues	8
Details	binding site for residue GOL B 406

Chain	Residue
A	PHE70
A	HOH730
B	ARG170
B	ASP257
B	ARG268
B	MLA403
B	HOH501
B	HOH664

site_id	AD6
Number of Residues	15
Details	binding site for residue 9Y7 C 501

Chain	Residue
C	LEU108
C	VAL109
C	ASN137
C	PRO138
C	VAL139
C	ASP140
C	ILE141
C	ARG168
C	GLU191
C	HIS192
C	TYR238
C	THR247
C	LEU322
C	NAI502
C	HOH724

site_id	AD7
Number of Residues	34
Details	binding site for residue NAI C 502

Chain	Residue
C	GLY28
C	ALA29
C	VAL30
C	ASP51
C	VAL52
C	ILE53
C	LYS56
C	THR94
C	ALA95
C	GLY96
C	ILE115
C	VAL135
C	SER136
C	ASN137
C	SER160
C	HIS192
C	THR247
C	ILE251
C	9Y7501
C	HOH608
C	HOH609
C	HOH629
C	HOH632
C	HOH636
C	HOH637
C	HOH649
C	HOH685
C	HOH693
C	HOH695
C	HOH725
C	HOH745
C	HOH747
C	HOH754
C	HOH767

site_id	AD8
Number of Residues	10
Details	binding site for residue MLA C 503

Chain	Residue
A	SER183
A	HIS185
C	ARG170
C	HIS185
C	VAL269
C	HOH620
C	HOH656
C	HOH658
C	HOH673
C	HOH715

site_id	AD9
Number of Residues	8
Details	binding site for residue GOL C 504

Chain	Residue
A	SER201
A	GOL504
A	HOH721
C	GLY207
C	VAL208
C	SER209
C	HOH606
C	HOH611

site_id	AE1
Number of Residues	4
Details	binding site for residue GOL C 505

Chain	Residue
C	LEU279
C	TYR280
C	VAL305
C	HOH674

site_id	AE2
Number of Residues	8
Details	binding site for residue GOL C 506

Chain	Residue
C	ASN163
C	ARG170
C	HIS270
C	PRO271
C	HOH616
C	HOH701
D	LEU69
D	PHE70

site_id	AE3
Number of Residues	14
Details	binding site for residue 9Y7 D 501

Chain	Residue
D	GLN99
D	LEU108
D	ASN137
D	PRO138
D	VAL139
D	ASP140
D	ILE141
D	ARG168
D	GLU191
D	HIS192
D	THR247
D	LEU322
D	NAI502
D	HOH627

site_id	AE4
Number of Residues	30
Details	binding site for residue NAI D 502

Chain	Residue
C	GLU101
C	HOH642
D	GLY28
D	ALA29
D	VAL30
D	ASP51
D	VAL52
D	ILE53
D	THR94
D	ALA95
D	ILE115
D	VAL135
D	SER136
D	ASN137
D	SER160
D	HIS192
D	THR247
D	ILE251
D	9Y7501
D	HOH604
D	HOH610
D	HOH653
D	HOH658
D	HOH661
D	HOH662
D	HOH676
D	HOH694
D	HOH733
D	HOH748
D	HOH784

site_id	AE5
Number of Residues	10
Details	binding site for residue MLA D 503

Chain	Residue
B	SER183
B	HIS185
B	HOH538
D	ARG170
D	HIS185
D	VAL269
D	HOH635
D	HOH648
D	HOH675
D	HOH722

site_id	AE6
Number of Residues	12
Details	binding site for residue GOL D 504

Chain	Residue
B	GLY202
B	ASN204
B	GLY207
B	GOL405
D	SER201
D	GLY202
D	MET203
D	ASN204
D	GLY207
D	SER209
D	HOH601
D	HOH709

site_id	AE7
Number of Residues	5
Details	binding site for residue GOL D 505

Chain	Residue
C	GLN65
C	HOH702
D	TYR171
D	GLU175
D	HOH830

site_id	AE8
Number of Residues	5
Details	binding site for residue GOL D 506

Chain	Residue
D	LEU279
D	TYR280
D	VAL305
D	HOH710
D	HOH816

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	15
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)