SMTL ID : 1pj3.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: R.145, E.235, D.236, D.259 Ligands: PYR.2 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:E.235, A:D.236, A:D.259, PYR.2, H2O.9 MN.6: 5 residues within 4Å: Chain B: R.145, E.235, D.236, D.259 Ligands: PYR.7 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:E.235, B:D.236, B:D.259, PYR.7, H2O.22 MN.11: 5 residues within 4Å: Chain C: R.145, E.235, D.236, D.259 Ligands: PYR.12 5 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:E.235, C:D.236, C:D.259, PYR.12, H2O.37 MN.16: 5 residues within 4Å: Chain D: R.145, E.235, D.236, D.259 Ligands: PYR.17 5 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: D:E.235, D:D.236, D:D.259, PYR.17, H2O.42

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 12 residues within 4Å: Chain A: Y.92, R.145, L.147, K.163, E.235, D.236, D.259, N.401, N.446, N.447 Ligands: MN.1, NAD.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.163, A:N.401, A:N.447 Water bridges: A:Y.92, A:Y.92, A:N.446 Salt bridges: A:R.145, A:K.163 PYR.7: 12 residues within 4Å: Chain B: Y.92, R.145, L.147, K.163, E.235, D.236, D.259, N.401, N.446, N.447 Ligands: MN.6, NAD.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.163, B:N.401, B:N.447 Water bridges: B:Y.92, B:N.446 Salt bridges: B:R.145, B:K.163 PYR.12: 12 residues within 4Å: Chain C: Y.92, R.145, L.147, K.163, E.235, D.236, D.259, N.401, N.446, N.447 Ligands: MN.11, NAD.13 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.163, C:N.401, C:N.447 Salt bridges: C:R.145, C:K.163 PYR.17: 12 residues within 4Å: Chain D: Y.92, R.145, L.147, K.163, E.235, D.236, D.259, N.401, N.446, N.447 Ligands: MN.16, NAD.18 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:K.163, D:N.401, D:N.447 Water bridges: D:Y.92, D:N.446 Salt bridges: D:R.145, D:K.163

8 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.3: 28 residues within 4Å: Chain A: R.145, L.147, G.148, N.239, D.259, T.263, 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, L.378, L.399, S.400, N.401, G.426, G.445, N.446, N.447 Ligands: PYR.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:T.263 Hydrogen bonds: A:L.147, A:N.239, A:A.292, A:A.292, A:E.294, A:A.295, A:K.326, A:L.399, A:N.401, A:N.401, A:N.446, A:N.447 Water bridges: A:G.293, A:A.296, A:D.325, A:K.326, A:G.328 Salt bridges: A:R.145 NAD.4: 17 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: R.124, D.224, R.225, G.227 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:K.136, A:G.172, A:R.174, A:R.177, A:R.177, A:N.462, A:Y.532, A:Y.532, A:W.538 Water bridges: A:K.136, D:R.228 Salt bridges: A:R.522, A:R.536, A:R.536 NAD.8: 27 residues within 4Å: Chain B: R.145, L.147, G.148, N.239, D.259, T.263, L.290, G.291, A.292, G.293, E.294, A.295, D.325, K.326, V.372, A.373, G.374, A.375, L.378, L.399, S.400, N.401, G.426, G.445, N.446, N.447 Ligands: PYR.7 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:T.263 Hydrogen bonds: B:L.147, B:N.239, B:A.292, B:A.292, B:E.294, B:E.294, B:A.295, B:K.326, B:L.399, B:N.401, B:N.401, B:N.447 Water bridges: B:G.293, B:A.296, B:D.325, B:Q.342 Salt bridges: B:R.145 NAD.9: 18 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, W.538 Chain C: T.223, D.224, R.225, Y.226, G.227 16 PLIP interactions: 2 interactions with chain C, 14 interactions with chain B Water bridges: C:R.228, C:R.228 Hydrogen bonds: B:K.136, B:R.174, B:R.177, B:R.177, B:N.462, B:Y.532, B:R.536, B:W.538 Salt bridges: B:R.522, B:R.522, B:R.536 pi-Cation interactions: B:H.134, B:R.177, B:R.177 NAD.13: 27 residues within 4Å: Chain C: R.145, L.147, G.148, N.239, D.259, T.263, 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, L.399, S.400, N.401, G.426, G.445, N.446, N.447 Ligands: PYR.12 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:T.263 Hydrogen bonds: C:L.147, C:N.239, C:A.292, C:A.292, C:E.294, C:A.295, C:K.326, C:K.326, C:K.326, C:L.399, C:N.401, C:N.401, C:N.446, C:N.447 Water bridges: C:G.293, C:A.296, C:D.325 Salt bridges: C:R.145 NAD.14: 17 residues within 4Å: Chain B: D.224, R.225, Y.226, G.227 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, W.538 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:H.134, C:G.172, C:R.174, C:R.177, C:N.462, C:Y.532, C:W.538, B:Y.226 Salt bridges: C:R.522, C:R.536 pi-Cation interactions: C:R.177, C:R.177 Water bridges: B:R.225 NAD.18: 28 residues within 4Å: Chain D: R.145, L.147, G.148, N.239, D.259, T.263, 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, L.378, L.399, S.400, N.401, G.426, G.445, N.446, N.447 Ligands: PYR.17 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:T.263 Hydrogen bonds: D:L.147, D:N.239, D:A.292, D:A.292, D:E.294, D:E.294, D:A.295, D:D.325, D:K.326, D:L.399, D:N.401, D:N.401, D:N.447 Water bridges: D:G.293, D:A.296, D:D.325 Salt bridges: D:R.145 NAD.19: 17 residues within 4Å: Chain A: R.124, D.224, R.225, G.227 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 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.172, D:R.174, D:R.177, D:N.462, D:Y.532, D:W.538, A:Y.226 Water bridges: D:N.462 Salt bridges: 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 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.75 Water bridges: A:Q.44, A:R.47, A:N.51, A:N.72 Salt bridges: A:R.47, A:R.71 Hydrogen bonds: B:R.108 FUM.10: 7 residues within 4Å: Chain A: F.107, R.108 Chain B: Q.44, R.47, I.68, R.71, L.75 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.75 Water bridges: B:E.39, B:Q.44, B:R.47, A:R.108 Salt bridges: B:R.47, B:R.71 FUM.15: 8 residues within 4Å: Chain C: Q.44, R.47, Y.64, I.68, R.71, L.75 Chain D: F.107, R.108 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.75 Water bridges: C:E.39, C:Q.44, C:R.47, D:R.108 Salt bridges: C:R.47, C:R.71 FUM.20: 7 residues within 4Å: Chain C: F.107, R.108 Chain D: Q.44, R.47, I.68, R.71, L.75 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.75 Water bridges: D:E.39, D:Q.44 Salt bridges: D:R.47, D:R.71 Hydrogen bonds: C:R.108

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

2003-11-11

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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