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1PJL

Crystal structure of human m-NAD-ME in ternary complex with NAD and Lu3+

Functional Information from GO Data
ChainGOidnamespacecontents
A0004470molecular_functionmalic enzyme activity
A0004471molecular_functionmalate dehydrogenase (decarboxylating) (NAD+) activity
A0004473molecular_functionmalate dehydrogenase (decarboxylating) (NADP+) activity
A0005739cellular_componentmitochondrion
A0005759cellular_componentmitochondrial matrix
A0006090biological_processpyruvate metabolic process
A0006108biological_processmalate metabolic process
A0008948molecular_functionoxaloacetate decarboxylase activity
A0009055molecular_functionelectron transfer activity
A0016491molecular_functionoxidoreductase activity
A0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A0043231cellular_componentintracellular membrane-bounded organelle
A0046872molecular_functionmetal ion binding
A0051287molecular_functionNAD binding
A1902031biological_processregulation of NADP metabolic process
B0004470molecular_functionmalic enzyme activity
B0004471molecular_functionmalate dehydrogenase (decarboxylating) (NAD+) activity
B0004473molecular_functionmalate dehydrogenase (decarboxylating) (NADP+) activity
B0005739cellular_componentmitochondrion
B0005759cellular_componentmitochondrial matrix
B0006090biological_processpyruvate metabolic process
B0006108biological_processmalate metabolic process
B0008948molecular_functionoxaloacetate decarboxylase activity
B0009055molecular_functionelectron transfer activity
B0016491molecular_functionoxidoreductase activity
B0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B0043231cellular_componentintracellular membrane-bounded organelle
B0046872molecular_functionmetal ion binding
B0051287molecular_functionNAD binding
B1902031biological_processregulation of NADP metabolic process
C0004470molecular_functionmalic enzyme activity
C0004471molecular_functionmalate dehydrogenase (decarboxylating) (NAD+) activity
C0004473molecular_functionmalate dehydrogenase (decarboxylating) (NADP+) activity
C0005739cellular_componentmitochondrion
C0005759cellular_componentmitochondrial matrix
C0006090biological_processpyruvate metabolic process
C0006108biological_processmalate metabolic process
C0008948molecular_functionoxaloacetate decarboxylase activity
C0009055molecular_functionelectron transfer activity
C0016491molecular_functionoxidoreductase activity
C0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
C0043231cellular_componentintracellular membrane-bounded organelle
C0046872molecular_functionmetal ion binding
C0051287molecular_functionNAD binding
C1902031biological_processregulation of NADP metabolic process
D0004470molecular_functionmalic enzyme activity
D0004471molecular_functionmalate dehydrogenase (decarboxylating) (NAD+) activity
D0004473molecular_functionmalate dehydrogenase (decarboxylating) (NADP+) activity
D0005739cellular_componentmitochondrion
D0005759cellular_componentmitochondrial matrix
D0006090biological_processpyruvate metabolic process
D0006108biological_processmalate metabolic process
D0008948molecular_functionoxaloacetate decarboxylase activity
D0009055molecular_functionelectron transfer activity
D0016491molecular_functionoxidoreductase activity
D0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
D0043231cellular_componentintracellular membrane-bounded organelle
D0046872molecular_functionmetal ion binding
D0051287molecular_functionNAD binding
D1902031biological_processregulation of NADP metabolic process
E0004470molecular_functionmalic enzyme activity
E0004471molecular_functionmalate dehydrogenase (decarboxylating) (NAD+) activity
E0004473molecular_functionmalate dehydrogenase (decarboxylating) (NADP+) activity
E0005739cellular_componentmitochondrion
E0005759cellular_componentmitochondrial matrix
E0006090biological_processpyruvate metabolic process
E0006108biological_processmalate metabolic process
E0008948molecular_functionoxaloacetate decarboxylase activity
E0009055molecular_functionelectron transfer activity
E0016491molecular_functionoxidoreductase activity
E0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
E0043231cellular_componentintracellular membrane-bounded organelle
E0046872molecular_functionmetal ion binding
E0051287molecular_functionNAD binding
E1902031biological_processregulation of NADP metabolic process
F0004470molecular_functionmalic enzyme activity
F0004471molecular_functionmalate dehydrogenase (decarboxylating) (NAD+) activity
F0004473molecular_functionmalate dehydrogenase (decarboxylating) (NADP+) activity
F0005739cellular_componentmitochondrion
F0005759cellular_componentmitochondrial matrix
F0006090biological_processpyruvate metabolic process
F0006108biological_processmalate metabolic process
F0008948molecular_functionoxaloacetate decarboxylase activity
F0009055molecular_functionelectron transfer activity
F0016491molecular_functionoxidoreductase activity
F0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
F0043231cellular_componentintracellular membrane-bounded organelle
F0046872molecular_functionmetal ion binding
F0051287molecular_functionNAD binding
F1902031biological_processregulation of NADP metabolic process
G0004470molecular_functionmalic enzyme activity
G0004471molecular_functionmalate dehydrogenase (decarboxylating) (NAD+) activity
G0004473molecular_functionmalate dehydrogenase (decarboxylating) (NADP+) activity
G0005739cellular_componentmitochondrion
G0005759cellular_componentmitochondrial matrix
G0006090biological_processpyruvate metabolic process
G0006108biological_processmalate metabolic process
G0008948molecular_functionoxaloacetate decarboxylase activity
G0009055molecular_functionelectron transfer activity
G0016491molecular_functionoxidoreductase activity
G0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
G0043231cellular_componentintracellular membrane-bounded organelle
G0046872molecular_functionmetal ion binding
G0051287molecular_functionNAD binding
G1902031biological_processregulation of NADP metabolic process
H0004470molecular_functionmalic enzyme activity
H0004471molecular_functionmalate dehydrogenase (decarboxylating) (NAD+) activity
H0004473molecular_functionmalate dehydrogenase (decarboxylating) (NADP+) activity
H0005739cellular_componentmitochondrion
H0005759cellular_componentmitochondrial matrix
H0006090biological_processpyruvate metabolic process
H0006108biological_processmalate metabolic process
H0008948molecular_functionoxaloacetate decarboxylase activity
H0009055molecular_functionelectron transfer activity
H0016491molecular_functionoxidoreductase activity
H0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
H0043231cellular_componentintracellular membrane-bounded organelle
H0046872molecular_functionmetal ion binding
H0051287molecular_functionNAD binding
H1902031biological_processregulation of NADP metabolic process
Functional Information from PDB Data
site_idAC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE LU A 604
ChainResidue
AGLU255
AASP256
AASP279

site_idAC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE LU B 1604
ChainResidue
BGLU1255
BASP1256
BASP1279

site_idAC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE LU C 2604
ChainResidue
CGLU2255
CASP2256
CASP2279

site_idAC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE LU D 3604
ChainResidue
DGLU3255
DASP3256
DASP3279

site_idAC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE LU E 4604
ChainResidue
EGLU4255
EASP4256
EASP4279

site_idAC6
Number of Residues3
DetailsBINDING SITE FOR RESIDUE LU F 5604
ChainResidue
FGLU5255
FASP5256
FASP5279

site_idAC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE LU G 6604
ChainResidue
GGLU6255
GASP6256
GASP6279

site_idAC8
Number of Residues3
DetailsBINDING SITE FOR RESIDUE LU H 7604
ChainResidue
HGLU7255
HASP7256
HASP7279

site_idAC9
Number of Residues21
DetailsBINDING SITE FOR RESIDUE NAD A 601
ChainResidue
AARG165
AASN259
ATHR283
ALEU310
AALA312
AGLY313
AGLU314
AALA315
AASP345
ALYS346
AVAL392
AALA393
AGLY394
AALA395
ALEU398
ALEU419
ASER420
AASN421
AGLY446
AGLY465
AASN467

site_idBC1
Number of Residues10
DetailsBINDING SITE FOR RESIDUE NAD A 602
ChainResidue
AHIS154
AGLY192
AILE193
AARG194
AARG197
AILE479
ALEU480
AARG542
ATYR552
AARG556

site_idBC2
Number of Residues20
DetailsBINDING SITE FOR RESIDUE NAD B 1601
ChainResidue
BASN1259
BTHR1283
BLEU1310
BALA1312
BGLY1313
BGLU1314
BALA1315
BASP1345
BLYS1346
BVAL1392
BALA1393
BGLY1394
BALA1395
BLEU1398
BLEU1419
BSER1420
BASN1421
BGLY1465
BASN1467
BHOH8059

site_idBC3
Number of Residues12
DetailsBINDING SITE FOR RESIDUE NAD B 1602
ChainResidue
BHIS1154
BLYS1156
BGLY1192
BILE1193
BARG1194
BARG1197
BILE1479
BLEU1480
BASN1482
BARG1542
BTYR1552
BARG1556

site_idBC4
Number of Residues21
DetailsBINDING SITE FOR RESIDUE NAD C 2601
ChainResidue
CGLY2394
CALA2395
CLEU2398
CLEU2419
CSER2420
CASN2421
CGLY2446
CGLY2465
CASN2467
CARG2165
CASN2259
CTHR2283
CLEU2310
CALA2312
CGLY2313
CGLU2314
CALA2315
CASP2345
CLYS2346
CVAL2392
CALA2393

site_idBC5
Number of Residues11
DetailsBINDING SITE FOR RESIDUE NAD C 2602
ChainResidue
CHIS2154
CGLY2192
CILE2193
CARG2194
CARG2197
CILE2479
CLEU2480
CASN2482
CARG2542
CTYR2552
CARG2556

site_idBC6
Number of Residues22
DetailsBINDING SITE FOR RESIDUE NAD D 3601
ChainResidue
DARG3165
DASN3259
DTHR3283
DLEU3310
DGLY3311
DALA3312
DGLY3313
DGLU3314
DALA3315
DASP3345
DLYS3346
DVAL3392
DALA3393
DGLY3394
DALA3395
DLEU3398
DLEU3419
DSER3420
DASN3421
DGLY3446
DGLY3465
DASN3467

site_idBC7
Number of Residues10
DetailsBINDING SITE FOR RESIDUE NAD D 3602
ChainResidue
DHIS3154
DLYS3156
DGLY3192
DILE3193
DARG3194
DILE3479
DLEU3480
DARG3542
DTYR3552
DARG3556

site_idBC8
Number of Residues23
DetailsBINDING SITE FOR RESIDUE NAD E 4601
ChainResidue
EARG4165
EASN4259
ETHR4283
ELEU4310
EGLY4311
EALA4312
EGLY4313
EGLU4314
EALA4315
EPHE4344
EASP4345
ELYS4346
EVAL4392
EALA4393
EGLY4394
EALA4395
ELEU4398
ELEU4419
ESER4420
EASN4421
EGLY4446
EGLY4465
EASN4467

site_idBC9
Number of Residues10
DetailsBINDING SITE FOR RESIDUE NAD E 4602
ChainResidue
EHIS4154
ELYS4156
EGLY4192
EILE4193
EARG4194
EARG4197
ELEU4480
EARG4542
ETYR4552
EARG4556

site_idCC1
Number of Residues21
DetailsBINDING SITE FOR RESIDUE NAD F 5601
ChainResidue
FARG5165
FASN5259
FTHR5283
FLEU5310
FGLY5311
FALA5312
FGLY5313
FGLU5314
FALA5315
FASP5345
FLYS5346
FVAL5392
FALA5393
FGLY5394
FALA5395
FLEU5398
FLEU5419
FASN5421
FGLY5446
FGLY5465
FASN5467

site_idCC2
Number of Residues8
DetailsBINDING SITE FOR RESIDUE NAD F 5602
ChainResidue
FGLY5192
FILE5193
FARG5194
FARG5197
FILE5479
FLEU5480
FARG5542
FARG5556

site_idCC3
Number of Residues21
DetailsBINDING SITE FOR RESIDUE NAD G 6601
ChainResidue
GARG6165
GASN6259
GTHR6283
GLEU6310
GGLY6311
GALA6312
GGLY6313
GGLU6314
GALA6315
GASP6345
GLYS6346
GALA6393
GGLY6394
GALA6395
GLEU6398
GLEU6419
GSER6420
GASN6421
GGLY6446
GGLY6465
GASN6467

site_idCC4
Number of Residues9
DetailsBINDING SITE FOR RESIDUE NAD G 6602
ChainResidue
GGLY6192
GILE6193
GARG6194
GARG6197
GILE6479
GLEU6480
GARG6542
GTYR6552
GARG6556

site_idCC5
Number of Residues19
DetailsBINDING SITE FOR RESIDUE NAD H 7601
ChainResidue
HARG7165
HTHR7283
HLEU7310
HGLY7311
HALA7312
HGLY7313
HGLU7314
HALA7315
HASP7345
HLYS7346
HVAL7392
HALA7393
HALA7395
HLEU7398
HLEU7419
HASN7421
HGLY7446
HGLY7465
HASN7467

site_idCC6
Number of Residues8
DetailsBINDING SITE FOR RESIDUE NAD H 7602
ChainResidue
HILE7193
HARG7194
HARG7197
HILE7479
HLEU7480
HARG7542
HTYR7552
HARG7556

Functional Information from PROSITE/UniProt
site_idPS00331
Number of Residues17
DetailsMALIC_ENZYMES Malic enzymes signature. FnDDiqGTAaVaLAGLL
ChainResidueDetails
APHE276-LEU292

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues8
DetailsACT_SITE: Proton donor => ECO:0000269|PubMed:12962632
ChainResidueDetails
ATYR112
BTYR1112
CTYR2112
DTYR3112
ETYR4112
FTYR5112
GTYR6112
HTYR7112

site_idSWS_FT_FI2
Number of Residues8
DetailsACT_SITE: Proton acceptor => ECO:0000269|PubMed:12962632
ChainResidueDetails
ALYS183
BLYS1183
CLYS2183
DLYS3183
ELYS4183
FLYS5183
GLYS6183
HLYS7183

site_idSWS_FT_FI3
Number of Residues16
DetailsBINDING: BINDING => ECO:0000269|PubMed:12121650, ECO:0000269|PubMed:12962632
ChainResidueDetails
AARG67
EARG4091
FARG5067
FARG5091
GARG6067
GARG6091
HARG7067
HARG7091
AARG91
BARG1067
BARG1091
CARG2067
CARG2091
DARG3067
DARG3091
EARG4067

site_idSWS_FT_FI4
Number of Residues24
DetailsBINDING: BINDING => ECO:0000269|PubMed:12962632
ChainResidueDetails
AARG165
DARG3165
DASN3421
DASN3466
EARG4165
EASN4421
EASN4466
FARG5165
FASN5421
FASN5466
GARG6165
AASN421
GASN6421
GASN6466
HARG7165
HASN7421
HASN7466
AASN466
BARG1165
BASN1421
BASN1466
CARG2165
CASN2421
CASN2466

site_idSWS_FT_FI5
Number of Residues24
DetailsBINDING: BINDING => ECO:0000269|PubMed:10700286, ECO:0000269|PubMed:12121650, ECO:0000269|PubMed:12962632
ChainResidueDetails
AGLU255
DGLU3255
DASP3256
DASP3279
EGLU4255
EASP4256
EASP4279
FGLU5255
FASP5256
FASP5279
GGLU6255
AASP256
GASP6256
GASP6279
HGLU7255
HASP7256
HASP7279
AASP279
BGLU1255
BASP1256
BASP1279
CGLU2255
CASP2256
CASP2279

site_idSWS_FT_FI6
Number of Residues16
DetailsBINDING: BINDING => ECO:0000269|PubMed:10700286, ECO:0000269|PubMed:12962632
ChainResidueDetails
AASN259
EGLY4311
FASN5259
FGLY5311
GASN6259
GGLY6311
HASN7259
HGLY7311
AGLY311
BASN1259
BGLY1311
CASN2259
CGLY2311
DASN3259
DGLY3311
EASN4259

site_idSWS_FT_FI7
Number of Residues40
DetailsMOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861
ChainResidueDetails
ALYS156
BLYS1346
CLYS2156
CLYS2224
CLYS2240
CLYS2272
CLYS2346
DLYS3156
DLYS3224
DLYS3240
DLYS3272
ALYS224
DLYS3346
ELYS4156
ELYS4224
ELYS4240
ELYS4272
ELYS4346
FLYS5156
FLYS5224
FLYS5240
FLYS5272
ALYS240
FLYS5346
GLYS6156
GLYS6224
GLYS6240
GLYS6272
GLYS6346
HLYS7156
HLYS7224
HLYS7240
HLYS7272
ALYS272
HLYS7346
ALYS346
BLYS1156
BLYS1224
BLYS1240
BLYS1272

Catalytic Information from CSA
site_idCSA1
Number of Residues3
DetailsAnnotated By Reference To The Literature 1do8
ChainResidueDetails
AASP278
ALYS183
ATYR112

site_idCSA2
Number of Residues3
DetailsAnnotated By Reference To The Literature 1do8
ChainResidueDetails
BLYS1183
BASP1278
BTYR1112

site_idCSA3
Number of Residues3
DetailsAnnotated By Reference To The Literature 1do8
ChainResidueDetails
CASP2278
CLYS2183
CTYR2112

site_idCSA4
Number of Residues3
DetailsAnnotated By Reference To The Literature 1do8
ChainResidueDetails
DASP3278
DTYR3112
DLYS3183

site_idCSA5
Number of Residues3
DetailsAnnotated By Reference To The Literature 1do8
ChainResidueDetails
EASP4278
ETYR4112
ELYS4183

site_idCSA6
Number of Residues3
DetailsAnnotated By Reference To The Literature 1do8
ChainResidueDetails
FTYR5112
FLYS5183
FASP5278

site_idCSA7
Number of Residues3
DetailsAnnotated By Reference To The Literature 1do8
ChainResidueDetails
GTYR6112
GLYS6183
GASP6278

site_idCSA8
Number of Residues3
DetailsAnnotated By Reference To The Literature 1do8
ChainResidueDetails
HASP7278
HLYS7183
HTYR7112

site_idMCSA1
Number of Residues8
DetailsM-CSA 21
ChainResidueDetails
ATYR112electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
AARG165electrostatic stabiliser, hydrogen bond donor
ALYS183electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
AGLU255metal ligand
AASP256metal ligand
AASP278hydrogen bond acceptor, proton acceptor, proton donor
AASP279metal ligand
AASN421electrostatic stabiliser, hydrogen bond donor

site_idMCSA2
Number of Residues8
DetailsM-CSA 21
ChainResidueDetails
BTYR1112electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
BARG1165electrostatic stabiliser, hydrogen bond donor
BLYS1183electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
BGLU1255metal ligand
BASP1256metal ligand
BASP1278hydrogen bond acceptor, proton acceptor, proton donor
BASP1279metal ligand
BASN1421electrostatic stabiliser, hydrogen bond donor

site_idMCSA3
Number of Residues8
DetailsM-CSA 21
ChainResidueDetails
CTYR2112electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
CARG2165electrostatic stabiliser, hydrogen bond donor
CLYS2183electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
CGLU2255metal ligand
CASP2256metal ligand
CASP2278hydrogen bond acceptor, proton acceptor, proton donor
CASP2279metal ligand
CASN2421electrostatic stabiliser, hydrogen bond donor

site_idMCSA4
Number of Residues8
DetailsM-CSA 21
ChainResidueDetails
DTYR3112electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
DARG3165electrostatic stabiliser, hydrogen bond donor
DLYS3183electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
DGLU3255metal ligand
DASP3256metal ligand
DASP3278hydrogen bond acceptor, proton acceptor, proton donor
DASP3279metal ligand
DASN3421electrostatic stabiliser, hydrogen bond donor

site_idMCSA5
Number of Residues8
DetailsM-CSA 21
ChainResidueDetails
ETYR4112electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
EARG4165electrostatic stabiliser, hydrogen bond donor
ELYS4183electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
EGLU4255metal ligand
EASP4256metal ligand
EASP4278hydrogen bond acceptor, proton acceptor, proton donor
EASP4279metal ligand
EASN4421electrostatic stabiliser, hydrogen bond donor

site_idMCSA6
Number of Residues8
DetailsM-CSA 21
ChainResidueDetails
FTYR5112electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
FARG5165electrostatic stabiliser, hydrogen bond donor
FLYS5183electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
FGLU5255metal ligand
FASP5256metal ligand
FASP5278hydrogen bond acceptor, proton acceptor, proton donor
FASP5279metal ligand
FASN5421electrostatic stabiliser, hydrogen bond donor

site_idMCSA7
Number of Residues8
DetailsM-CSA 21
ChainResidueDetails
GTYR6112electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
GARG6165electrostatic stabiliser, hydrogen bond donor
GLYS6183electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
GGLU6255metal ligand
GASP6256metal ligand
GASP6278hydrogen bond acceptor, proton acceptor, proton donor
GASP6279metal ligand
GASN6421electrostatic stabiliser, hydrogen bond donor

site_idMCSA8
Number of Residues8
DetailsM-CSA 21
ChainResidueDetails
HTYR7112electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
HARG7165electrostatic stabiliser, hydrogen bond donor
HLYS7183electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
HGLU7255metal ligand
HASP7256metal ligand
HASP7278hydrogen bond acceptor, proton acceptor, proton donor
HASP7279metal ligand
HASN7421electrostatic stabiliser, hydrogen bond donor

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PDB entries from 2024-07-24

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