SMTL ID : 1pj4.1

Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a pentary complex with natural substrate malate, ATP, Mn++, and allosteric activator fumarate.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x MLT: D-MALATE(Non-covalent)

MLT.1: 12 residues within 4Å: Chain A: Y.92, T.93, R.145, L.147, K.163, E.235, D.236, D.259, N.401, N.446, N.447 Ligands: MN.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.92, A:K.163, A:N.401, A:N.446, A:N.447 Water bridges: A:R.145, A:R.145, A:K.163 Salt bridges: A:R.145, A:K.163 MLT.6: 12 residues within 4Å: Chain B: Y.92, T.93, R.145, L.147, K.163, E.235, D.236, D.259, N.401, N.446, N.447 Ligands: MN.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.92, B:K.163, B:N.401, B:N.446, B:N.447 Salt bridges: B:R.145, B:K.163 MLT.11: 12 residues within 4Å: Chain C: Y.92, T.93, R.145, L.147, K.163, E.235, D.236, D.259, N.401, N.446, N.447 Ligands: MN.12 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.163, C:N.401, C:N.446, C:N.447 Water bridges: C:K.163 Salt bridges: C:R.145, C:K.163 MLT.16: 12 residues within 4Å: Chain D: Y.92, T.93, R.145, L.147, K.163, E.235, D.236, D.259, N.401, N.446, N.447 Ligands: MN.17 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:K.163, D:D.258, D:N.401, D:N.446, D:N.447 Water bridges: D:R.145, D:K.163, D:T.263 Salt bridges: D:R.145, D:K.163

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

MN.2: 5 residues within 4Å: Chain A: R.145, E.235, D.236, D.259 Ligands: MLT.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.235, A:D.236, A:D.259, H2O.1 MN.7: 4 residues within 4Å: Chain B: E.235, D.236, D.259 Ligands: MLT.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.235, B:D.236, B:D.259, H2O.7 MN.12: 5 residues within 4Å: Chain C: R.145, E.235, D.236, D.259 Ligands: MLT.11 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.235, C:D.236, C:D.259, H2O.15 MN.17: 5 residues within 4Å: Chain D: R.145, E.235, D.236, D.259 Ligands: MLT.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.235, D:D.236, D:D.259, H2O.20

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

ATP.3: 15 residues within 4Å: Chain A: R.145, N.239, L.290, G.291, A.292, G.293, E.294, A.295, D.325, K.326, V.372, A.373, G.374, A.375, S.400 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:N.239, A:A.292, A:A.292, A:E.294, A:E.294, A:A.295, A:K.326, A:G.374, A:S.400 Water bridges: A:R.145, A:L.147, A:N.239, A:G.293, A:G.293, A:D.325, A:A.375, A:N.401 Salt bridges: A:R.145, A:R.145 ATP.4: 14 residues within 4Å: Chain A: H.134, K.136, G.172, I.173, R.174, R.177, I.459, L.460, N.462, R.522, Y.532, R.536, W.538 Chain D: D.224 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:H.134, A:K.136, A:G.172, A:R.174, A:R.177, A:N.462, A:Y.532, A:W.538 Salt bridges: A:H.134, A:R.177, A:R.522, A:R.536 pi-Cation interactions: A:R.177, A:R.177 ATP.8: 15 residues within 4Å: Chain B: R.145, N.239, L.290, G.291, A.292, G.293, E.294, A.295, D.325, K.326, V.372, A.373, G.374, A.375, S.400 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:N.239, B:A.292, B:A.292, B:E.294, B:E.294, B:E.294, B:A.295, B:K.326, B:K.326, B:G.374, B:S.400 Water bridges: B:G.293, B:A.296, B:K.326, B:K.326 Salt bridges: B:R.145, B:R.145, B:R.145 ATP.9: 13 residues within 4Å: Chain B: H.134, K.136, G.172, I.173, R.174, R.177, I.459, L.460, N.462, R.522, Y.532, R.536 Chain C: D.224 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:H.134, B:G.172, B:R.174, B:R.177, B:N.462, B:Y.532 Salt bridges: B:H.134, B:R.177, B:R.522, B:R.536 pi-Cation interactions: B:R.177, B:R.177 ATP.13: 16 residues within 4Å: Chain C: R.145, L.147, N.239, L.290, G.291, A.292, G.293, E.294, A.295, D.325, K.326, V.372, A.373, G.374, A.375, S.400 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:L.147, C:N.239, C:A.292, C:A.292, C:E.294, C:E.294, C:A.295, C:D.325, C:K.326, C:K.326, C:K.326, C:G.374 Water bridges: C:R.145, C:G.293, C:L.399, C:N.401, C:N.401, C:N.401 Salt bridges: C:R.145, C:R.145 ATP.14: 13 residues within 4Å: Chain B: D.224 Chain C: H.134, K.136, G.172, I.173, R.174, R.177, I.459, L.460, N.462, R.522, Y.532, R.536 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:H.134, C:G.172, C:R.174, C:R.177, C:R.177, C:N.462, C:W.538 Salt bridges: C:H.134, C:R.522, C:R.536 pi-Cation interactions: C:R.177 ATP.18: 16 residues within 4Å: Chain D: R.145, N.239, L.290, G.291, A.292, G.293, E.294, A.295, F.324, D.325, K.326, V.372, A.373, G.374, A.375, S.400 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:N.239, D:A.292, D:A.292, D:E.294, D:E.294, D:E.294, D:A.295, D:K.326, D:G.374, D:S.400 Water bridges: D:R.145, D:N.239, D:G.293, D:A.296, D:D.325, D:D.325, D:N.401, D:N.401 Salt bridges: D:R.145, D:R.145 ATP.19: 14 residues within 4Å: Chain A: D.224 Chain D: H.134, K.136, G.172, I.173, R.174, R.177, I.459, L.460, N.462, R.522, Y.532, R.536, W.538 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:H.134, D:H.134, D:G.172, D:R.174, D:R.177, D:N.462, D:W.538 Water bridges: D:N.462, A:T.223 Salt bridges: D:R.177, D:R.522, D:R.536 pi-Cation interactions: D:R.177

4 x FUM: FUMARIC ACID(Non-covalent)

FUM.5: 7 residues within 4Å: Chain A: Q.44, R.47, I.68, R.71, L.75 Chain B: F.107, R.108 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.75 Hydrogen bonds: A:Q.44, B:R.108 Water bridges: A:N.72 Salt bridges: A:R.47, A:R.71 FUM.10: 8 residues within 4Å: Chain A: F.107, R.108 Chain B: Q.44, R.47, Y.64, I.68, R.71, L.75 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.75 Water bridges: B:Q.44, B:Y.64 Salt bridges: B:R.47, B:R.71 Hydrogen bonds: A:R.108 FUM.15: 7 residues within 4Å: Chain C: Q.44, R.47, I.68, R.71, L.75 Chain D: F.107, R.108 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.75 Water bridges: C:E.39, C:Q.44 Salt bridges: C:R.47, C:R.71 Hydrogen bonds: D:R.108 FUM.20: 7 residues within 4Å: Chain C: F.107, R.108 Chain D: Q.44, R.47, I.68, R.71, L.75 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.75 Hydrogen bonds: D:Q.44, C:R.108 Water bridges: D:R.47, D:N.72 Salt bridges: D:R.47, D:R.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tao, X. et al., Crystal structures of substrate complexes of malic enzyme and insights into the catalytic mechanism. Structure (2003)

Release Date

2003-09-30

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

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