SMTL ID : 1gz3.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 18 residues within 4Å: Chain A: R.146, L.148, N.240, L.291, G.292, A.293, G.294, E.295, A.296, F.325, D.326, K.327, V.373, A.374, G.375, A.376, L.379, S.401 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.240, A:A.293, A:E.295, A:E.295, A:E.295, A:A.296, A:K.327 Water bridges: A:R.146, A:R.146, A:R.146, A:N.240, A:D.260, A:G.294, A:L.400, A:S.401, A:N.402 Salt bridges: A:R.146, A:R.146 ATP.5: 18 residues within 4Å: Chain B: R.146, N.240, L.291, G.292, A.293, G.294, E.295, A.296, F.325, D.326, K.327, V.373, A.374, G.375, A.376, L.379, S.401 Ligands: OXL.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:N.240, B:A.293, B:A.293, B:E.295, B:E.295, B:A.296, B:K.327, B:S.401 Water bridges: B:R.146, B:R.146, B:N.240, B:G.294, B:D.326 Salt bridges: B:R.146, B:R.146 ATP.9: 16 residues within 4Å: Chain C: R.146, N.240, L.291, G.292, A.293, G.294, E.295, A.296, F.325, D.326, K.327, V.373, A.374, G.375, A.376, S.401 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:N.240, C:A.293, C:A.293, C:E.295, C:E.295, C:A.296, C:K.327 Water bridges: C:R.146, C:N.240, C:T.264, C:G.294, C:D.326, C:L.400, C:N.402 Salt bridges: C:R.146, C:R.146 ATP.13: 17 residues within 4Å: Chain D: R.146, N.240, L.291, G.292, A.293, G.294, E.295, A.296, F.325, D.326, K.327, V.373, A.374, G.375, A.376, L.379, S.401 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:N.240, D:A.293, D:A.293, D:E.295, D:E.295, D:E.295, D:A.296, D:K.327 Water bridges: D:R.146, D:R.146, D:R.146, D:R.146, D:N.240, D:G.294, D:A.297, D:D.326, D:D.326, D:A.376, D:N.402 Salt bridges: D:R.146, D:R.146

4 x OXL: OXALATE ION(Non-covalent)

OXL.2: 11 residues within 4Å: Chain A: Y.93, R.146, L.148, K.164, E.236, D.237, D.260, N.402, N.447, N.448 Ligands: MN.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.402, A:N.447, A:N.448 Water bridges: A:R.146, A:R.146, A:K.164, A:N.447, A:N.448 Salt bridges: A:R.146, A:K.164 OXL.6: 12 residues within 4Å: Chain B: Y.93, R.146, L.148, K.164, E.236, D.237, D.260, N.402, N.447, N.448 Ligands: ATP.5, MN.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:L.148, B:N.402, B:N.447, B:N.448 Water bridges: B:K.164, B:N.447, B:N.448 Salt bridges: B:R.146, B:K.164 OXL.10: 11 residues within 4Å: Chain C: Y.93, R.146, L.148, K.164, E.236, D.237, D.260, N.402, N.447, N.448 Ligands: MN.11 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:N.402, C:N.447, C:N.448 Water bridges: C:R.146, C:R.146, C:K.164, C:K.164, C:N.402, C:N.447 Salt bridges: C:R.146, C:K.164, C:K.164 OXL.14: 11 residues within 4Å: Chain D: Y.93, R.146, L.148, K.164, E.236, D.237, D.260, N.402, N.447, N.448 Ligands: MN.15 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:N.402, D:N.447, D:N.448 Water bridges: D:R.146, D:R.146, D:K.164, D:N.402, D:N.448 Salt bridges: D:R.146, D:K.164

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 5 residues within 4Å: Chain A: R.146, E.236, D.237, D.260 Ligands: OXL.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.236, A:D.237, A:D.260, H2O.11 MN.7: 5 residues within 4Å: Chain B: R.146, E.236, D.237, D.260 Ligands: OXL.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.236, B:D.237, B:D.260, H2O.22 MN.11: 6 residues within 4Å: Chain C: R.146, K.164, E.236, D.237, D.260 Ligands: OXL.10 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.236, C:D.237, C:D.260, H2O.33 MN.15: 5 residues within 4Å: Chain D: R.146, E.236, D.237, D.260 Ligands: OXL.14 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.236, D:D.237, D:D.260, H2O.45

4 x FUM: FUMARIC ACID(Non-covalent)

FUM.4: 7 residues within 4Å: Chain A: Q.45, R.48, I.69, R.72, L.76 Chain B: F.108, R.109 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:F.108, A:R.48 Hydrophobic interactions: A:L.76 Salt bridges: A:R.48, A:R.72 FUM.8: 7 residues within 4Å: Chain A: F.108, R.109 Chain B: Q.45, R.48, I.69, R.72, L.76 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.76 Water bridges: B:N.16, B:Q.45, A:F.108 Salt bridges: B:R.48, B:R.72 FUM.12: 7 residues within 4Å: Chain C: Q.45, R.48, I.69, R.72, L.76 Chain D: F.108, R.109 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.76 Water bridges: C:N.16, D:F.108 Salt bridges: C:R.48, C:R.72 FUM.16: 7 residues within 4Å: Chain C: F.108, R.109 Chain D: Q.45, R.48, I.69, R.72, L.76 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.76 Water bridges: D:N.16, D:Y.65, D:N.73 Salt bridges: D:R.48, D:R.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., Molecular Mechanism for the Regulation of Human Mitochondrial Nad(P)+-Dependent Malic Enzyme by ATP and Fumarate. Structure (2002)

Release Date

2003-05-22

Peptides

NAD-dependent malic enzyme, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NAD-dependent malic enzyme, mitochondrial