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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

7XDG

Cryo-EM structures of human mitochondrial NAD(P)+-dependent malic enzyme in a ternary complex with NAD+ and allosteric inhibitor MDSA

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 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
DetailsActive site: {"description":"Proton donor","evidences":[{"source":"PubMed","id":"12962632","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues4
DetailsActive site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"12962632","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues8
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12121650","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12962632","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1GZ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GZ4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ4","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues8
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"10700286","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12962632","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1DO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QR6","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"10700286","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12121650","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12962632","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1DO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GZ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1GZ4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ4","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"10700286","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12962632","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1DO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QR6","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PDB","id":"1DO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QR6","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PDB","id":"1DO8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EFL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QR6","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues8
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12962632","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1PJ2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1PJ4","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues20
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
Catalytic Information from CSA
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

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PDB entries from 2025-07-16

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