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4OKN

Crystal structure of human muscle L-lactate dehydrogenase, ternary complex with NADH and oxalate

Functional Information from GO Data
ChainGOidnamespacecontents
A0003824molecular_functioncatalytic activity
A0004459molecular_functionL-lactate dehydrogenase activity
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005829cellular_componentcytosol
A0006089biological_processlactate metabolic process
A0006090biological_processpyruvate metabolic process
A0006096biological_processglycolytic process
A0016020cellular_componentmembrane
A0016491molecular_functionoxidoreductase activity
A0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A0019752biological_processcarboxylic acid metabolic process
A0042802molecular_functionidentical protein binding
A0045296molecular_functioncadherin binding
A0070062cellular_componentextracellular exosome
A1990204cellular_componentoxidoreductase complex
B0003824molecular_functioncatalytic activity
B0004459molecular_functionL-lactate dehydrogenase activity
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005739cellular_componentmitochondrion
B0005829cellular_componentcytosol
B0006089biological_processlactate metabolic process
B0006090biological_processpyruvate metabolic process
B0006096biological_processglycolytic process
B0016020cellular_componentmembrane
B0016491molecular_functionoxidoreductase activity
B0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B0019752biological_processcarboxylic acid metabolic process
B0042802molecular_functionidentical protein binding
B0045296molecular_functioncadherin binding
B0070062cellular_componentextracellular exosome
B1990204cellular_componentoxidoreductase complex
C0003824molecular_functioncatalytic activity
C0004459molecular_functionL-lactate dehydrogenase activity
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005737cellular_componentcytoplasm
C0005739cellular_componentmitochondrion
C0005829cellular_componentcytosol
C0006089biological_processlactate metabolic process
C0006090biological_processpyruvate metabolic process
C0006096biological_processglycolytic process
C0016020cellular_componentmembrane
C0016491molecular_functionoxidoreductase activity
C0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
C0019752biological_processcarboxylic acid metabolic process
C0042802molecular_functionidentical protein binding
C0045296molecular_functioncadherin binding
C0070062cellular_componentextracellular exosome
C1990204cellular_componentoxidoreductase complex
D0003824molecular_functioncatalytic activity
D0004459molecular_functionL-lactate dehydrogenase activity
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005737cellular_componentcytoplasm
D0005739cellular_componentmitochondrion
D0005829cellular_componentcytosol
D0006089biological_processlactate metabolic process
D0006090biological_processpyruvate metabolic process
D0006096biological_processglycolytic process
D0016020cellular_componentmembrane
D0016491molecular_functionoxidoreductase activity
D0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
D0019752biological_processcarboxylic acid metabolic process
D0042802molecular_functionidentical protein binding
D0045296molecular_functioncadherin binding
D0070062cellular_componentextracellular exosome
D1990204cellular_componentoxidoreductase complex
E0003824molecular_functioncatalytic activity
E0004459molecular_functionL-lactate dehydrogenase activity
E0005515molecular_functionprotein binding
E0005634cellular_componentnucleus
E0005737cellular_componentcytoplasm
E0005739cellular_componentmitochondrion
E0005829cellular_componentcytosol
E0006089biological_processlactate metabolic process
E0006090biological_processpyruvate metabolic process
E0006096biological_processglycolytic process
E0016020cellular_componentmembrane
E0016491molecular_functionoxidoreductase activity
E0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
E0019752biological_processcarboxylic acid metabolic process
E0042802molecular_functionidentical protein binding
E0045296molecular_functioncadherin binding
E0070062cellular_componentextracellular exosome
E1990204cellular_componentoxidoreductase complex
F0003824molecular_functioncatalytic activity
F0004459molecular_functionL-lactate dehydrogenase activity
F0005515molecular_functionprotein binding
F0005634cellular_componentnucleus
F0005737cellular_componentcytoplasm
F0005739cellular_componentmitochondrion
F0005829cellular_componentcytosol
F0006089biological_processlactate metabolic process
F0006090biological_processpyruvate metabolic process
F0006096biological_processglycolytic process
F0016020cellular_componentmembrane
F0016491molecular_functionoxidoreductase activity
F0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
F0019752biological_processcarboxylic acid metabolic process
F0042802molecular_functionidentical protein binding
F0045296molecular_functioncadherin binding
F0070062cellular_componentextracellular exosome
F1990204cellular_componentoxidoreductase complex
G0003824molecular_functioncatalytic activity
G0004459molecular_functionL-lactate dehydrogenase activity
G0005515molecular_functionprotein binding
G0005634cellular_componentnucleus
G0005737cellular_componentcytoplasm
G0005739cellular_componentmitochondrion
G0005829cellular_componentcytosol
G0006089biological_processlactate metabolic process
G0006090biological_processpyruvate metabolic process
G0006096biological_processglycolytic process
G0016020cellular_componentmembrane
G0016491molecular_functionoxidoreductase activity
G0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
G0019752biological_processcarboxylic acid metabolic process
G0042802molecular_functionidentical protein binding
G0045296molecular_functioncadherin binding
G0070062cellular_componentextracellular exosome
G1990204cellular_componentoxidoreductase complex
H0003824molecular_functioncatalytic activity
H0004459molecular_functionL-lactate dehydrogenase activity
H0005515molecular_functionprotein binding
H0005634cellular_componentnucleus
H0005737cellular_componentcytoplasm
H0005739cellular_componentmitochondrion
H0005829cellular_componentcytosol
H0006089biological_processlactate metabolic process
H0006090biological_processpyruvate metabolic process
H0006096biological_processglycolytic process
H0016020cellular_componentmembrane
H0016491molecular_functionoxidoreductase activity
H0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
H0019752biological_processcarboxylic acid metabolic process
H0042802molecular_functionidentical protein binding
H0045296molecular_functioncadherin binding
H0070062cellular_componentextracellular exosome
H1990204cellular_componentoxidoreductase complex
Functional Information from PDB Data
site_idAC1
Number of Residues28
DetailsBINDING SITE FOR RESIDUE NAI A 401
ChainResidue
AGLY29
AALA98
AARG99
AGLN100
APHE119
AILE120
AVAL136
AASN138
ASER161
AHIS193
ATHR248
AALA30
AILE252
AOXL402
AHOH502
AHOH540
AHOH556
AHOH561
AHOH584
AHOH585
GASN108
AVAL31
AASP52
AVAL53
AILE54
ATHR95
AALA96
AGLY97

site_idAC2
Number of Residues9
DetailsBINDING SITE FOR RESIDUE OXL A 402
ChainResidue
AGLN100
AARG106
AASN138
AARG169
AHIS193
AALA238
ATHR248
ANAI401
AHOH556

site_idAC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 A 403
ChainResidue
AASN164
ASER167
AARG171
APRO272
BLEU70

site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE OXL B 401
ChainResidue
BASN138
BARG169
BHIS193
BTHR248
BHOH592

site_idAC5
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SO4 B 402
ChainResidue
BARG171
BHIS186
BHOH516
BHOH519
BHOH541
BHOH546
DLEU183
DHIS186

site_idAC6
Number of Residues11
DetailsBINDING SITE FOR RESIDUE KAN B 403
ChainResidue
BASP52
BVAL53
BALA96
BGLY97
BARG99
BARG112
BILE116
BPHE119
BILE120
HGLU55
HHOH556

site_idAC7
Number of Residues30
DetailsBINDING SITE FOR RESIDUE NAI C 401
ChainResidue
CGLY29
CALA30
CVAL31
CASP52
CVAL53
CILE54
CLYS57
CTHR95
CALA96
CGLY97
CALA98
CARG99
CASN113
CILE120
CVAL136
CASN138
CSER161
CHIS193
CTHR248
CILE252
COXL402
CHOH503
CHOH509
CHOH525
CHOH528
CHOH544
CHOH575
CHOH579
CHOH593
CHOH604

site_idAC8
Number of Residues10
DetailsBINDING SITE FOR RESIDUE OXL C 402
ChainResidue
CLEU165
CARG169
CHIS193
CALA238
CTHR248
CNAI401
CHOH544
CGLN100
CARG106
CASN138

site_idAC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 C 403
ChainResidue
CASN164
CSER167
CARG171
CPRO272
DLEU70

site_idBC1
Number of Residues34
DetailsBINDING SITE FOR RESIDUE NAI D 401
ChainResidue
DGLY29
DALA30
DVAL31
DASP52
DVAL53
DILE54
DLYS57
DTHR95
DALA96
DGLY97
DALA98
DARG99
DGLN100
DASN113
DILE116
DILE120
DVAL136
DASN138
DSER161
DLEU165
DHIS193
DTHR248
DILE252
DOXL402
DHOH501
DHOH525
DHOH550
DHOH563
DHOH589
DHOH590
DHOH593
DHOH629
EGLY103
EASN108

site_idBC2
Number of Residues9
DetailsBINDING SITE FOR RESIDUE OXL D 402
ChainResidue
DGLN100
DARG106
DASN138
DARG169
DHIS193
DALA238
DTHR248
DNAI401
DHOH589

site_idBC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE SO4 D 403
ChainResidue
CLEU70
DASN164
DSER167
DARG171
DPRO272
DHOH596

site_idBC4
Number of Residues30
DetailsBINDING SITE FOR RESIDUE NAI E 401
ChainResidue
EGLY29
EALA30
EVAL31
EASP52
EVAL53
EILE54
ELYS57
ETHR95
EALA96
EGLY97
EALA98
EARG99
EGLN100
EASN113
EILE116
EILE120
EVAL136
EASN138
ESER161
ELEU165
EHIS193
ETHR248
EILE252
EOXL402
EHOH504
EHOH509
EHOH514
EHOH547
EHOH571
EHOH575

site_idBC5
Number of Residues9
DetailsBINDING SITE FOR RESIDUE OXL E 402
ChainResidue
EGLN100
EARG106
EASN138
EARG169
EHIS193
EALA238
ETHR248
ENAI401
EHOH514

site_idBC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 E 403
ChainResidue
EASN164
ESER167
EARG171
EPRO272

site_idBC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE SO4 E 404
ChainResidue
DGLY97
DALA98
DILE116
DHOH563
DHOH578
EASN108

site_idBC8
Number of Residues28
DetailsBINDING SITE FOR RESIDUE NAI F 401
ChainResidue
CGLN111
FGLY29
FALA30
FVAL31
FASP52
FVAL53
FILE54
FLYS57
FTHR95
FALA96
FGLY97
FALA98
FARG99
FILE116
FVAL136
FASN138
FSER161
FHIS193
FTHR248
FILE252
FOXL402
FHOH501
FHOH503
FHOH544
FHOH566
FHOH567
FHOH589
FHOH596

site_idBC9
Number of Residues9
DetailsBINDING SITE FOR RESIDUE OXL F 402
ChainResidue
FGLN100
FARG106
FASN138
FARG169
FHIS193
FALA238
FTHR248
FNAI401
FHOH596

site_idCC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 F 403
ChainResidue
ELEU70
FASN164
FSER167
FARG171
FPRO272

site_idCC2
Number of Residues27
DetailsBINDING SITE FOR RESIDUE NAI G 401
ChainResidue
GGLY29
GALA30
GVAL31
GASP52
GVAL53
GILE54
GLYS57
GTHR95
GALA96
GGLY97
GALA98
GARG99
GGLN100
GILE116
GVAL136
GASN138
GSER161
GLEU165
GHIS193
GTHR248
GILE252
GOXL402
GHOH502
GHOH510
GHOH515
GHOH530
GHOH576

site_idCC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE OXL G 402
ChainResidue
GGLN100
GARG106
GASN138
GARG169
GHIS193
GALA238
GTHR248
GNAI401

site_idCC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 G 403
ChainResidue
GASN164
GSER167
GARG171
GPRO272
HLEU70

site_idCC5
Number of Residues26
DetailsBINDING SITE FOR RESIDUE NAI H 401
ChainResidue
HGLY29
HALA30
HVAL31
HASP52
HILE54
HTHR95
HALA96
HGLY97
HALA98
HARG99
HILE116
HPHE119
HILE120
HVAL136
HASN138
HSER161
HLEU165
HHIS193
HTHR248
HILE252
HOXL402
HHOH502
HHOH507
HHOH517
HHOH521
HHOH550

site_idCC6
Number of Residues8
DetailsBINDING SITE FOR RESIDUE OXL H 402
ChainResidue
HGLN100
HARG106
HASN138
HARG169
HHIS193
HALA238
HTHR248
HNAI401

site_idCC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE SO4 H 403
ChainResidue
GLEU70
HASN164
HSER167
HARG171
HTRP188
HPRO272

Functional Information from PROSITE/UniProt
site_idPS00064
Number of Residues7
DetailsL_LDH L-lactate dehydrogenase active site. LGEHGDS
ChainResidueDetails
ALEU190-SER196

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues8
DetailsACT_SITE: Proton acceptor
ChainResidueDetails
AHIS193
BHIS193
CHIS193
DHIS193
EHIS193
FHIS193
GHIS193
HHIS193

site_idSWS_FT_FI2
Number of Residues16
DetailsBINDING: BINDING => ECO:0000269|PubMed:11276087
ChainResidueDetails
AGLY29
EARG99
FGLY29
FARG99
GGLY29
GARG99
HGLY29
HARG99
AARG99
BGLY29
BARG99
CGLY29
CARG99
DGLY29
DARG99
EGLY29

site_idSWS_FT_FI3
Number of Residues32
DetailsBINDING:
ChainResidueDetails
AARG106
CASN138
CARG169
CTHR248
DARG106
DASN138
DARG169
DTHR248
EARG106
EASN138
EARG169
AASN138
ETHR248
FARG106
FASN138
FARG169
FTHR248
GARG106
GASN138
GARG169
GTHR248
HARG106
AARG169
HASN138
HARG169
HTHR248
ATHR248
BARG106
BASN138
BARG169
BTHR248
CARG106

site_idSWS_FT_FI4
Number of Residues8
DetailsMOD_RES: N-acetylalanine => ECO:0000269|Ref.10, ECO:0007744|PubMed:19413330, ECO:0007744|PubMed:22223895
ChainResidueDetails
AALA2
BALA2
CALA2
DALA2
EALA2
FALA2
GALA2
HALA2

site_idSWS_FT_FI5
Number of Residues24
DetailsMOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P06151
ChainResidueDetails
ALYS5
DLYS5
DLYS118
DLYS318
ELYS5
ELYS118
ELYS318
FLYS5
FLYS118
FLYS318
GLYS5
ALYS118
GLYS118
GLYS318
HLYS5
HLYS118
HLYS318
ALYS318
BLYS5
BLYS118
BLYS318
CLYS5
CLYS118
CLYS318

site_idSWS_FT_FI6
Number of Residues8
DetailsMOD_RES: Phosphotyrosine => ECO:0007744|PubMed:19690332
ChainResidueDetails
ATYR10
BTYR10
CTYR10
DTYR10
ETYR10
FTYR10
GTYR10
HTYR10

site_idSWS_FT_FI7
Number of Residues24
DetailsMOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861
ChainResidueDetails
ALYS14
DLYS14
DLYS81
DLYS126
ELYS14
ELYS81
ELYS126
FLYS14
FLYS81
FLYS126
GLYS14
ALYS81
GLYS81
GLYS126
HLYS14
HLYS81
HLYS126
ALYS126
BLYS14
BLYS81
BLYS126
CLYS14
CLYS81
CLYS126

site_idSWS_FT_FI8
Number of Residues8
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163
ChainResidueDetails
ATHR18
BTHR18
CTHR18
DTHR18
ETHR18
FTHR18
GTHR18
HTHR18

site_idSWS_FT_FI9
Number of Residues8
DetailsMOD_RES: N6-acetyllysine; alternate => ECO:0007744|PubMed:19608861
ChainResidueDetails
ALYS57
BLYS57
CLYS57
DLYS57
ELYS57
FLYS57
GLYS57
HLYS57

site_idSWS_FT_FI10
Number of Residues24
DetailsMOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P06151
ChainResidueDetails
ALYS224
DLYS224
DLYS232
DLYS243
ELYS224
ELYS232
ELYS243
FLYS224
FLYS232
FLYS243
GLYS224
ALYS232
GLYS232
GLYS243
HLYS224
HLYS232
HLYS243
ALYS243
BLYS224
BLYS232
BLYS243
CLYS224
CLYS232
CLYS243

site_idSWS_FT_FI11
Number of Residues8
DetailsMOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P06151
ChainResidueDetails
ATYR239
BTYR239
CTYR239
DTYR239
ETYR239
FTYR239
GTYR239
HTYR239

site_idSWS_FT_FI12
Number of Residues16
DetailsMOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P04642
ChainResidueDetails
ATHR309
ETHR322
FTHR309
FTHR322
GTHR309
GTHR322
HTHR309
HTHR322
ATHR322
BTHR309
BTHR322
CTHR309
CTHR322
DTHR309
DTHR322
ETHR309

site_idSWS_FT_FI13
Number of Residues8
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569
ChainResidueDetails
ASER310
BSER310
CSER310
DSER310
ESER310
FSER310
GSER310
HSER310

site_idSWS_FT_FI14
Number of Residues16
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:28112733
ChainResidueDetails
ALYS57
FLYS57
GLYS57
HLYS57
BLYS57
CLYS57
DLYS57
ELYS57

218853

PDB entries from 2024-04-24

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