Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6Q0D

CRYSTAL STRUCTURE OF LDHA IN COMPLEX WITH COMPOUND NCGC00384414-01 AT 2.05 A RESOLUTION

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	binding site for residue PO4 A 501

Chain	Residue
A	ARG170
A	HIS185
A	HOH613
A	HOH617
A	HOH652
C	HIS185
C	HOH626

site_id	AC2
Number of Residues	16
Details	binding site for residue P8M A 502

Chain	Residue
A	ASN137
A	PRO138
A	VAL139
A	ASP140
A	ILE141
A	ARG168
A	GLU191
A	HIS192
A	GLY193
A	ASP194
A	ALA237
A	THR247
A	LEU322
A	NAI503
A	ARG105
A	LEU108

site_id	AC3
Number of Residues	28
Details	binding site for residue NAI A 503

Chain	Residue
A	GLY28
A	ALA29
A	VAL30
A	ASP51
A	VAL52
A	ILE53
A	THR94
A	ALA95
A	GLY96
A	ARG98
A	ILE115
A	ILE119
A	VAL135
A	SER136
A	ASN137
A	HIS192
A	THR247
A	ILE251
A	P8M502
A	HOH609
A	HOH612
A	HOH619
A	HOH636
A	HOH637
A	HOH646
A	HOH663
A	HOH666
A	HOH687

site_id	AC4
Number of Residues	5
Details	binding site for residue GOL B 500

Chain	Residue
B	SER78
B	GLY79
B	HOH612
B	HOH620
B	HOH645

site_id	AC5
Number of Residues	7
Details	binding site for residue PO4 B 501

Chain	Residue
B	ARG170
B	HIS185
B	HOH669
B	HOH672
B	HOH674
D	HIS185
D	HOH630

site_id	AC6
Number of Residues	16
Details	binding site for residue P8M B 502

Chain	Residue
B	LEU108
B	ASN137
B	PRO138
B	VAL139
B	ASP140
B	ILE141
B	LEU164
B	ARG168
B	GLU191
B	HIS192
B	TYR238
B	THR247
B	LEU322
B	ILE325
B	NAI503
E	GLU328

site_id	AC7
Number of Residues	25
Details	binding site for residue NAI B 503

Chain	Residue
B	HOH627
B	HOH648
B	HOH650
B	HOH670
B	HOH692
B	GLY28
B	ALA29
B	VAL30
B	ASP51
B	VAL52
B	ILE53
B	THR94
B	ALA95
B	GLY96
B	ILE115
B	ILE119
B	VAL135
B	SER136
B	ASN137
B	HIS192
B	THR247
B	ILE251
B	P8M502
B	HOH611
B	HOH622

site_id	AC8
Number of Residues	5
Details	binding site for residue GOL C 500

Chain	Residue
C	GLU54
C	SER78
C	GLY79
C	LYS80
C	ASP81

site_id	AC9
Number of Residues	7
Details	binding site for residue PO4 C 501

Chain	Residue
A	HIS185
A	HOH620
C	ARG170
C	HIS185
C	HOH602
C	HOH648
C	HOH665

site_id	AD1
Number of Residues	19
Details	binding site for residue P8M C 502

Chain	Residue
C	ARG105
C	LEU106
C	VAL109
C	ASN137
C	PRO138
C	VAL139
C	ASP140
C	ILE141
C	ARG168
C	GLU191
C	HIS192
C	GLY193
C	ILE241
C	THR247
C	LEU322
C	ILE325
C	NAI503
C	HOH633
F	GLU328

site_id	AD2
Number of Residues	25
Details	binding site for residue NAI C 503

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	ASN137
C	LEU164
C	HIS192
C	THR247
C	ILE251
C	P8M502
C	HOH601
C	HOH603
C	HOH624
C	HOH630
C	HOH649
C	HOH651

site_id	AD3
Number of Residues	7
Details	binding site for residue PO4 D 501

Chain	Residue
B	HIS185
B	HOH647
D	ARG170
D	HIS185
D	HOH613
D	HOH621
D	HOH653

site_id	AD4
Number of Residues	19
Details	binding site for residue P8M D 502

Chain	Residue
D	ARG105
D	LEU108
D	VAL109
D	ASN137
D	PRO138
D	VAL139
D	ASP140
D	ILE141
D	LEU164
D	ARG168
D	GLU191
D	HIS192
D	ALA237
D	TYR238
D	THR247
D	LEU322
D	ILE325
D	NAI503
D	HOH682

site_id	AD5
Number of Residues	24
Details	binding site for residue NAI D 503

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	HIS192
D	THR247
D	ILE251
D	P8M502
D	HOH609
D	HOH615
D	HOH646
D	HOH651
D	HOH660

site_id	AD6
Number of Residues	6
Details	binding site for residue GOL E 401

Chain	Residue
E	PRO198
E	TRP200
E	THR308
E	GLU310
E	GLU311
E	ARG314

site_id	AD7
Number of Residues	2
Details	binding site for residue GOL E 402

Chain	Residue
E	LYS41
E	HOH517

site_id	AD8
Number of Residues	5
Details	binding site for residue GOL E 403

Chain	Residue
E	ASP5
E	ILE8
E	TYR9
E	ASN10
F	LYS304

site_id	AD9
Number of Residues	9
Details	binding site for residue PO4 E 404

Chain	Residue
E	ARG170
E	HIS185
E	HOH513
E	HOH531
E	HOH538
E	HOH550
E	HOH551
F	HIS185
F	HOH613

site_id	AE1
Number of Residues	20
Details	binding site for residue P8M E 405

Chain	Residue
B	GLU328
E	ARG105
E	LEU106
E	LEU108
E	VAL109
E	ASN137
E	PRO138
E	VAL139
E	ASP140
E	ILE141
E	LEU164
E	ARG168
E	GLU191
E	HIS192
E	THR247
E	LEU322
E	ILE325
E	NAI406
E	HOH599
E	HOH612

site_id	AE2
Number of Residues	31
Details	binding site for residue NAI E 406

Chain	Residue
E	GLY28
E	ALA29
E	VAL30
E	ASP51
E	VAL52
E	ILE53
E	THR94
E	ALA95
E	GLY96
E	ARG98
E	ILE115
E	ILE119
E	VAL135
E	SER136
E	ASN137
E	LEU164
E	HIS192
E	THR247
E	ILE251
E	P8M405
E	HOH506
E	HOH507
E	HOH510
E	HOH524
E	HOH532
E	HOH536
E	HOH540
E	HOH586
E	HOH593
E	HOH600
E	HOH626

site_id	AE3
Number of Residues	1
Details	binding site for residue GOL F 500

Chain	Residue
F	ALA313

site_id	AE4
Number of Residues	9
Details	binding site for residue PO4 F 501

Chain	Residue
E	HIS185
E	HOH534
F	ARG170
F	HIS185
F	HOH606
F	HOH642
F	HOH645
F	HOH655
F	HOH727

site_id	AE5
Number of Residues	16
Details	binding site for residue P8M F 502

Chain	Residue
C	GLU328
F	LEU108
F	VAL109
F	ASN137
F	PRO138
F	VAL139
F	ASP140
F	ILE141
F	LEU164
F	ARG168
F	GLU191
F	HIS192
F	THR247
F	LEU322
F	NAI503
F	HOH722

site_id	AE6
Number of Residues	32
Details	binding site for residue NAI F 503

Chain	Residue
F	GLY28
F	ALA29
F	VAL30
F	ASP51
F	VAL52
F	ILE53
F	THR94
F	ALA95
F	GLY96
F	ARG98
F	ILE115
F	PHE118
F	ILE119
F	VAL135
F	SER136
F	ASN137
F	HIS192
F	THR247
F	ILE251
F	P8M502
F	HOH603
F	HOH604
F	HOH615
F	HOH630
F	HOH643
F	HOH644
F	HOH656
F	HOH662
F	HOH678
F	HOH693
F	HOH705
F	HOH712

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	6
Details	Active site: {"description":"Proton acceptor"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	174
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11276087","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	24
Details	Binding site: {}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	6
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	18
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	6
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	18
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	6
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	6
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	18
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	6
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P06151","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	12
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P04642","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	6
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	12
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)