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1GZ3

Molecular mechanism for the regulation of human mitochondrial NAD(P)+-dependent malic enzyme by ATP and fumarate

Functional Information from GO Data
ChainGOidnamespacecontents
A0003824molecular_functioncatalytic activity
A0004470molecular_functionmalic enzyme activity
A0004471molecular_functionmalate dehydrogenase (decarboxylating) (NAD+) activity
A0004473molecular_functionmalate dehydrogenase (decarboxylating) (NADP+) activity
A0005739cellular_componentmitochondrion
A0005759cellular_componentmitochondrial matrix
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
A0046872molecular_functionmetal ion binding
A0051287molecular_functionNAD binding
A1902031biological_processregulation of NADP metabolic process
B0003824molecular_functioncatalytic activity
B0004470molecular_functionmalic enzyme activity
B0004471molecular_functionmalate dehydrogenase (decarboxylating) (NAD+) activity
B0004473molecular_functionmalate dehydrogenase (decarboxylating) (NADP+) activity
B0005739cellular_componentmitochondrion
B0005759cellular_componentmitochondrial matrix
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
B0046872molecular_functionmetal ion binding
B0051287molecular_functionNAD binding
B1902031biological_processregulation of NADP metabolic process
C0003824molecular_functioncatalytic activity
C0004470molecular_functionmalic enzyme activity
C0004471molecular_functionmalate dehydrogenase (decarboxylating) (NAD+) activity
C0004473molecular_functionmalate dehydrogenase (decarboxylating) (NADP+) activity
C0005739cellular_componentmitochondrion
C0005759cellular_componentmitochondrial matrix
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
C0046872molecular_functionmetal ion binding
C0051287molecular_functionNAD binding
C1902031biological_processregulation of NADP metabolic process
D0003824molecular_functioncatalytic activity
D0004470molecular_functionmalic enzyme activity
D0004471molecular_functionmalate dehydrogenase (decarboxylating) (NAD+) activity
D0004473molecular_functionmalate dehydrogenase (decarboxylating) (NADP+) activity
D0005739cellular_componentmitochondrion
D0005759cellular_componentmitochondrial matrix
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
D0046872molecular_functionmetal ion binding
D0051287molecular_functionNAD binding
D1902031biological_processregulation of NADP metabolic process
Functional Information from PDB Data
site_idAC1
Number of Residues13
DetailsBINDING SITE FOR RESIDUE OXL A 603
ChainResidue
AARG165
AMN604
AHOH2129
AHOH2208
AHOH2264
ALEU167
ALYS183
AGLU255
AASP256
AASP279
AASN421
AASN466
AASN467

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MN A 604
ChainResidue
AARG165
AGLU255
AASP256
AASP279
AOXL603
AHOH2265

site_idAC3
Number of Residues11
DetailsBINDING SITE FOR RESIDUE OXL B 603
ChainResidue
BARG165
BLYS183
BGLU255
BASP256
BASP279
BASN421
BASN466
BASN467
BMN604
BHOH2234
BHOH2286

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MN B 604
ChainResidue
BARG165
BGLU255
BASP256
BASP279
BOXL603
BHOH2287

site_idAC5
Number of Residues13
DetailsBINDING SITE FOR RESIDUE OXL C 603
ChainResidue
CARG165
CLEU167
CLYS183
CGLU255
CASP256
CASP279
CASN421
CASN466
CASN467
CMN604
CHOH2249
CHOH2293
CHOH2298

site_idAC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MN C 604
ChainResidue
CARG165
CGLU255
CASP256
CASP279
COXL603
CHOH2299

site_idAC7
Number of Residues12
DetailsBINDING SITE FOR RESIDUE OXL D 603
ChainResidue
DARG165
DLEU167
DLYS183
DGLU255
DASP256
DASP279
DASN421
DASN466
DASN467
DMN604
DHOH2293
DHOH2298

site_idAC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MN D 604
ChainResidue
DARG165
DGLU255
DASP256
DASP279
DOXL603
DHOH2299

site_idAC9
Number of Residues24
DetailsBINDING SITE FOR RESIDUE ATP A 601
ChainResidue
AARG165
ALEU167
AASN259
AALA312
AGLY313
AGLU314
AALA315
AASP345
ALYS346
AVAL392
AALA393
AGLY394
AALA395
ALEU398
ASER420
AHOH2116
AHOH2186
AHOH2256
AHOH2258
AHOH2259
AHOH2260
AHOH2261
AHOH2262
AHOH2263

site_idBC1
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FUM A 605
ChainResidue
AARG91
AHOH2028
AHOH2032
AHOH2266
AHOH2267
BPHE127
AGLN64
AARG67

site_idBC2
Number of Residues24
DetailsBINDING SITE FOR RESIDUE ATP B 601
ChainResidue
BARG165
BASN259
BGLY311
BALA312
BGLY313
BGLU314
BALA315
BASP345
BLYS346
BVAL392
BALA393
BALA395
BLEU398
BHOH2274
BHOH2275
BHOH2276
BHOH2277
BHOH2278
BHOH2280
BHOH2281
BHOH2282
BHOH2283
BHOH2284
BHOH2285

site_idBC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FUM B 605
ChainResidue
APHE127
AARG128
BGLN64
BARG67
BARG91
BHOH2288
BHOH2289
BHOH2290

site_idBC4
Number of Residues25
DetailsBINDING SITE FOR RESIDUE ATP C 601
ChainResidue
CARG165
CASN259
CGLY311
CALA312
CGLY313
CGLU314
CALA315
CASP345
CLYS346
CVAL392
CALA393
CGLY394
CALA395
CSER420
CHOH2136
CHOH2152
CHOH2289
CHOH2290
CHOH2291
CHOH2292
CHOH2293
CHOH2294
CHOH2295
CHOH2296
CHOH2297

site_idBC5
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FUM C 605
ChainResidue
CGLN64
CARG67
CARG91
CHOH2037
CHOH2043
CHOH2300
DPHE127
DARG128

site_idBC6
Number of Residues24
DetailsBINDING SITE FOR RESIDUE ATP D 601
ChainResidue
DARG165
DASN259
DGLY311
DALA312
DGLY313
DGLU314
DALA315
DASP345
DLYS346
DVAL392
DALA393
DGLY394
DALA395
DLEU398
DHOH2287
DHOH2288
DHOH2289
DHOH2291
DHOH2292
DHOH2293
DHOH2294
DHOH2295
DHOH2296
DHOH2297

site_idBC7
Number of Residues8
DetailsBINDING SITE FOR RESIDUE FUM D 605
ChainResidue
CPHE127
DGLN64
DARG67
DILE88
DARG91
DHOH2031
DHOH2036
DHOH2300

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 Residues4
DetailsACT_SITE: Proton donor => ECO:0000269|PubMed:12962632
ChainResidueDetails
ATYR112
BTYR112
CTYR112
DTYR112

site_idSWS_FT_FI2
Number of Residues4
DetailsACT_SITE: Proton acceptor => ECO:0000269|PubMed:12962632
ChainResidueDetails
ALYS183
BLYS183
CLYS183
DLYS183

site_idSWS_FT_FI3
Number of Residues8
DetailsBINDING: BINDING => ECO:0000269|PubMed:12121650, ECO:0000269|PubMed:12962632, ECO:0007744|PDB:1GZ3, ECO:0007744|PDB:1GZ4, ECO:0007744|PDB:1PJ2, ECO:0007744|PDB:1PJ3, ECO:0007744|PDB:1PJ4
ChainResidueDetails
AARG67
AARG91
BARG67
BARG91
CARG67
CARG91
DARG67
DARG91

site_idSWS_FT_FI4
Number of Residues8
DetailsBINDING: BINDING => ECO:0000269|PubMed:10700286, ECO:0000269|PubMed:12962632, ECO:0007744|PDB:1DO8, ECO:0007744|PDB:1EFK, ECO:0007744|PDB:1EFL, ECO:0007744|PDB:1PJ3, ECO:0007744|PDB:1PJL, ECO:0007744|PDB:1QR6
ChainResidueDetails
AARG165
AALA312
BARG165
BALA312
CARG165
CALA312
DARG165
DALA312

site_idSWS_FT_FI5
Number of Residues12
DetailsBINDING: BINDING => ECO:0000269|PubMed:10700286, ECO:0000269|PubMed:12121650, ECO:0000269|PubMed:12962632, ECO:0007744|PDB:1DO8, ECO:0007744|PDB:1EFK, ECO:0007744|PDB:1EFL, ECO:0007744|PDB:1GZ3, ECO:0007744|PDB:1GZ4, ECO:0007744|PDB:1PJ2, ECO:0007744|PDB:1PJ3, ECO:0007744|PDB:1PJ4
ChainResidueDetails
AGLU255
DGLU255
DASP256
DASP279
AASP256
AASP279
BGLU255
BASP256
BASP279
CGLU255
CASP256
CASP279

site_idSWS_FT_FI6
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:10700286, ECO:0000269|PubMed:12962632, ECO:0007744|PDB:1DO8, ECO:0007744|PDB:1EFK, ECO:0007744|PDB:1EFL, ECO:0007744|PDB:1PJ3, ECO:0007744|PDB:1QR6
ChainResidueDetails
AASN259
BASN259
CASN259
DASN259

site_idSWS_FT_FI7
Number of Residues4
DetailsBINDING: BINDING => ECO:0007744|PDB:1DO8, ECO:0007744|PDB:1EFK, ECO:0007744|PDB:1EFL, ECO:0007744|PDB:1PJ3, ECO:0007744|PDB:1QR6
ChainResidueDetails
AGLU314
BGLU314
CGLU314
DGLU314

site_idSWS_FT_FI8
Number of Residues4
DetailsBINDING: BINDING => ECO:0007744|PDB:1DO8, ECO:0007744|PDB:1EFK, ECO:0007744|PDB:1EFL, ECO:0007744|PDB:1PJ3, ECO:0007744|PDB:1PJL, ECO:0007744|PDB:1QR6
ChainResidueDetails
AALA315
BALA315
CALA315
DALA315

site_idSWS_FT_FI9
Number of Residues8
DetailsBINDING: BINDING => ECO:0000269|PubMed:12962632, ECO:0007744|PDB:1PJ2, ECO:0007744|PDB:1PJ4
ChainResidueDetails
AASN421
AASN466
BASN421
BASN466
CASN421
CASN466
DASN421
DASN466

site_idSWS_FT_FI10
Number of Residues20
DetailsMOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861
ChainResidueDetails
ALYS156
BLYS346
CLYS156
CLYS224
CLYS240
CLYS272
CLYS346
DLYS156
DLYS224
DLYS240
DLYS272
ALYS224
DLYS346
ALYS240
ALYS272
ALYS346
BLYS156
BLYS224
BLYS240
BLYS272

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
BASP278
BLYS183
BTYR112

site_idCSA3
Number of Residues3
DetailsAnnotated By Reference To The Literature 1do8
ChainResidueDetails
CASP278
CLYS183
CTYR112

site_idCSA4
Number of Residues3
DetailsAnnotated By Reference To The Literature 1do8
ChainResidueDetails
DASP278
DLYS183
DTYR112

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
BTYR112electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
BARG165electrostatic stabiliser, hydrogen bond donor
BLYS183electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
BGLU255metal ligand
BASP256metal ligand
BASP278hydrogen bond acceptor, proton acceptor, proton donor
BASP279metal ligand
BASN421electrostatic stabiliser, hydrogen bond donor

site_idMCSA3
Number of Residues8
DetailsM-CSA 21
ChainResidueDetails
CTYR112electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
CARG165electrostatic stabiliser, hydrogen bond donor
CLYS183electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
CGLU255metal ligand
CASP256metal ligand
CASP278hydrogen bond acceptor, proton acceptor, proton donor
CASP279metal ligand
CASN421electrostatic stabiliser, hydrogen bond donor

site_idMCSA4
Number of Residues8
DetailsM-CSA 21
ChainResidueDetails
DTYR112electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
DARG165electrostatic stabiliser, hydrogen bond donor
DLYS183electrostatic stabiliser, hydrogen bond donor, proton acceptor, proton donor, proton relay
DGLU255metal ligand
DASP256metal ligand
DASP278hydrogen bond acceptor, proton acceptor, proton donor
DASP279metal ligand
DASN421electrostatic stabiliser, hydrogen bond donor

238268

PDB entries from 2025-07-02

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