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6Q0D

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

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
Functional Information from PDB Data
site_idAC1
Number of Residues7
Detailsbinding site for residue PO4 A 501
ChainResidue
AARG170
AHIS185
AHOH613
AHOH617
AHOH652
CHIS185
CHOH626

site_idAC2
Number of Residues16
Detailsbinding site for residue P8M A 502
ChainResidue
AASN137
APRO138
AVAL139
AASP140
AILE141
AARG168
AGLU191
AHIS192
AGLY193
AASP194
AALA237
ATHR247
ALEU322
ANAI503
AARG105
ALEU108

site_idAC3
Number of Residues28
Detailsbinding site for residue NAI A 503
ChainResidue
AGLY28
AALA29
AVAL30
AASP51
AVAL52
AILE53
ATHR94
AALA95
AGLY96
AARG98
AILE115
AILE119
AVAL135
ASER136
AASN137
AHIS192
ATHR247
AILE251
AP8M502
AHOH609
AHOH612
AHOH619
AHOH636
AHOH637
AHOH646
AHOH663
AHOH666
AHOH687

site_idAC4
Number of Residues5
Detailsbinding site for residue GOL B 500
ChainResidue
BSER78
BGLY79
BHOH612
BHOH620
BHOH645

site_idAC5
Number of Residues7
Detailsbinding site for residue PO4 B 501
ChainResidue
BARG170
BHIS185
BHOH669
BHOH672
BHOH674
DHIS185
DHOH630

site_idAC6
Number of Residues16
Detailsbinding site for residue P8M B 502
ChainResidue
BLEU108
BASN137
BPRO138
BVAL139
BASP140
BILE141
BLEU164
BARG168
BGLU191
BHIS192
BTYR238
BTHR247
BLEU322
BILE325
BNAI503
EGLU328

site_idAC7
Number of Residues25
Detailsbinding site for residue NAI B 503
ChainResidue
BHOH627
BHOH648
BHOH650
BHOH670
BHOH692
BGLY28
BALA29
BVAL30
BASP51
BVAL52
BILE53
BTHR94
BALA95
BGLY96
BILE115
BILE119
BVAL135
BSER136
BASN137
BHIS192
BTHR247
BILE251
BP8M502
BHOH611
BHOH622

site_idAC8
Number of Residues5
Detailsbinding site for residue GOL C 500
ChainResidue
CGLU54
CSER78
CGLY79
CLYS80
CASP81

site_idAC9
Number of Residues7
Detailsbinding site for residue PO4 C 501
ChainResidue
AHIS185
AHOH620
CARG170
CHIS185
CHOH602
CHOH648
CHOH665

site_idAD1
Number of Residues19
Detailsbinding site for residue P8M C 502
ChainResidue
CARG105
CLEU106
CVAL109
CASN137
CPRO138
CVAL139
CASP140
CILE141
CARG168
CGLU191
CHIS192
CGLY193
CILE241
CTHR247
CLEU322
CILE325
CNAI503
CHOH633
FGLU328

site_idAD2
Number of Residues25
Detailsbinding site for residue NAI C 503
ChainResidue
CGLY28
CALA29
CVAL30
CASP51
CVAL52
CILE53
CTHR94
CALA95
CGLY96
CARG98
CILE115
CILE119
CVAL135
CASN137
CLEU164
CHIS192
CTHR247
CILE251
CP8M502
CHOH601
CHOH603
CHOH624
CHOH630
CHOH649
CHOH651

site_idAD3
Number of Residues7
Detailsbinding site for residue PO4 D 501
ChainResidue
BHIS185
BHOH647
DARG170
DHIS185
DHOH613
DHOH621
DHOH653

site_idAD4
Number of Residues19
Detailsbinding site for residue P8M D 502
ChainResidue
DARG105
DLEU108
DVAL109
DASN137
DPRO138
DVAL139
DASP140
DILE141
DLEU164
DARG168
DGLU191
DHIS192
DALA237
DTYR238
DTHR247
DLEU322
DILE325
DNAI503
DHOH682

site_idAD5
Number of Residues24
Detailsbinding site for residue NAI D 503
ChainResidue
DGLY28
DALA29
DVAL30
DASP51
DVAL52
DILE53
DTHR94
DALA95
DGLY96
DARG98
DILE115
DILE119
DVAL135
DSER136
DASN137
DHIS192
DTHR247
DILE251
DP8M502
DHOH609
DHOH615
DHOH646
DHOH651
DHOH660

site_idAD6
Number of Residues6
Detailsbinding site for residue GOL E 401
ChainResidue
EPRO198
ETRP200
ETHR308
EGLU310
EGLU311
EARG314

site_idAD7
Number of Residues2
Detailsbinding site for residue GOL E 402
ChainResidue
ELYS41
EHOH517

site_idAD8
Number of Residues5
Detailsbinding site for residue GOL E 403
ChainResidue
EASP5
EILE8
ETYR9
EASN10
FLYS304

site_idAD9
Number of Residues9
Detailsbinding site for residue PO4 E 404
ChainResidue
EARG170
EHIS185
EHOH513
EHOH531
EHOH538
EHOH550
EHOH551
FHIS185
FHOH613

site_idAE1
Number of Residues20
Detailsbinding site for residue P8M E 405
ChainResidue
BGLU328
EARG105
ELEU106
ELEU108
EVAL109
EASN137
EPRO138
EVAL139
EASP140
EILE141
ELEU164
EARG168
EGLU191
EHIS192
ETHR247
ELEU322
EILE325
ENAI406
EHOH599
EHOH612

site_idAE2
Number of Residues31
Detailsbinding site for residue NAI E 406
ChainResidue
EGLY28
EALA29
EVAL30
EASP51
EVAL52
EILE53
ETHR94
EALA95
EGLY96
EARG98
EILE115
EILE119
EVAL135
ESER136
EASN137
ELEU164
EHIS192
ETHR247
EILE251
EP8M405
EHOH506
EHOH507
EHOH510
EHOH524
EHOH532
EHOH536
EHOH540
EHOH586
EHOH593
EHOH600
EHOH626

site_idAE3
Number of Residues1
Detailsbinding site for residue GOL F 500
ChainResidue
FALA313

site_idAE4
Number of Residues9
Detailsbinding site for residue PO4 F 501
ChainResidue
EHIS185
EHOH534
FARG170
FHIS185
FHOH606
FHOH642
FHOH645
FHOH655
FHOH727

site_idAE5
Number of Residues16
Detailsbinding site for residue P8M F 502
ChainResidue
CGLU328
FLEU108
FVAL109
FASN137
FPRO138
FVAL139
FASP140
FILE141
FLEU164
FARG168
FGLU191
FHIS192
FTHR247
FLEU322
FNAI503
FHOH722

site_idAE6
Number of Residues32
Detailsbinding site for residue NAI F 503
ChainResidue
FGLY28
FALA29
FVAL30
FASP51
FVAL52
FILE53
FTHR94
FALA95
FGLY96
FARG98
FILE115
FPHE118
FILE119
FVAL135
FSER136
FASN137
FHIS192
FTHR247
FILE251
FP8M502
FHOH603
FHOH604
FHOH615
FHOH630
FHOH643
FHOH644
FHOH656
FHOH662
FHOH678
FHOH693
FHOH705
FHOH712

Functional Information from PROSITE/UniProt
site_idPS00064
Number of Residues7
DetailsL_LDH L-lactate dehydrogenase active site. LGEHGDS
ChainResidueDetails
ALEU189-SER195

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues6
DetailsACT_SITE: Proton acceptor
ChainResidueDetails
AHIS192
BHIS192
CHIS192
DHIS192
EHIS192
FHIS192

site_idSWS_FT_FI2
Number of Residues12
DetailsBINDING: BINDING => ECO:0000269|PubMed:11276087
ChainResidueDetails
DGLY28
DARG98
EGLY28
EARG98
FGLY28
FARG98
AGLY28
AARG98
BGLY28
BARG98
CGLY28
CARG98

site_idSWS_FT_FI3
Number of Residues24
DetailsBINDING:
ChainResidueDetails
BARG168
BTHR247
CARG105
CASN137
CARG168
CTHR247
DARG105
DASN137
DARG168
DTHR247
EARG105
EASN137
EARG168
ETHR247
FARG105
FASN137
FARG168
FTHR247
AARG105
AASN137
AARG168
ATHR247
BARG105
BASN137

site_idSWS_FT_FI4
Number of Residues6
DetailsMOD_RES: N-acetylalanine => ECO:0000269|Ref.10, ECO:0007744|PubMed:19413330, ECO:0007744|PubMed:22223895
ChainResidueDetails
AALA1
BALA1
CALA1
DALA1
EALA1
FALA1

site_idSWS_FT_FI5
Number of Residues18
DetailsMOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P06151
ChainResidueDetails
CLYS4
CLYS117
CLYS317
DLYS4
DLYS117
DLYS317
ELYS4
ELYS117
ELYS317
FLYS4
FLYS117
FLYS317
ALYS4
ALYS117
ALYS317
BLYS4
BLYS117
BLYS317

site_idSWS_FT_FI6
Number of Residues6
DetailsMOD_RES: Phosphotyrosine => ECO:0007744|PubMed:19690332
ChainResidueDetails
ATYR9
BTYR9
CTYR9
DTYR9
ETYR9
FTYR9

site_idSWS_FT_FI7
Number of Residues18
DetailsMOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861
ChainResidueDetails
CLYS13
CLYS80
CLYS125
DLYS13
DLYS80
DLYS125
ELYS13
ELYS80
ELYS125
FLYS13
FLYS80
FLYS125
BLYS80
BLYS125
ALYS13
ALYS80
ALYS125
BLYS13

site_idSWS_FT_FI8
Number of Residues6
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163
ChainResidueDetails
FTHR17
ATHR17
BTHR17
CTHR17
DTHR17
ETHR17

site_idSWS_FT_FI9
Number of Residues6
DetailsMOD_RES: N6-acetyllysine; alternate => ECO:0007744|PubMed:19608861
ChainResidueDetails
ELYS56
FLYS56
ALYS56
BLYS56
CLYS56
DLYS56

site_idSWS_FT_FI10
Number of Residues18
DetailsMOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P06151
ChainResidueDetails
CLYS223
CLYS231
CLYS242
DLYS223
DLYS231
DLYS242
ELYS223
ELYS231
ELYS242
FLYS223
FLYS231
FLYS242
ALYS223
ALYS231
ALYS242
BLYS223
BLYS231
BLYS242

site_idSWS_FT_FI11
Number of Residues6
DetailsMOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P06151
ChainResidueDetails
ATYR238
BTYR238
CTYR238
DTYR238
ETYR238
FTYR238

site_idSWS_FT_FI12
Number of Residues12
DetailsMOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P04642
ChainResidueDetails
DTHR308
DTHR321
ETHR308
ETHR321
FTHR308
FTHR321
ATHR321
BTHR321
CTHR321
ATHR308
BTHR308
CTHR308

site_idSWS_FT_FI13
Number of Residues6
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569
ChainResidueDetails
ASER309
BSER309
CSER309
DSER309
ESER309
FSER309

site_idSWS_FT_FI14
Number of Residues12
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:28112733
ChainResidueDetails
DLYS56
ELYS56
FLYS56
ALYS56
BLYS56
CLYS56

221051

PDB entries from 2024-06-12

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