SMTL ID : 1qr6.1

HUMAN MITOCHONDRIAL NAD(P)-DEPENDENT MALIC ENZYME

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 23 residues within 4Å: Chain A: R.165, N.259, T.283, L.310, G.311, A.312, G.313, E.314, A.315, F.344, D.345, K.346, V.392, A.393, G.394, A.395, L.398, L.419, S.420, N.421, G.446, G.465, N.467 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:T.283 Hydrogen bonds: A:N.259, A:A.312, A:A.312, A:G.313, A:E.314, A:E.314, A:A.315, A:K.346, A:N.421, A:N.421, A:N.421, A:G.465 Water bridges: A:R.165, A:R.165, A:G.313, A:A.316, A:D.345, A:N.467 Salt bridges: A:R.165, A:R.165 NAD.2: 19 residues within 4Å: Chain A: H.154, K.156, G.192, I.193, R.194, R.197, I.479, L.480, N.482, R.542, Y.552, R.556, W.558 Chain D: T.243, D.244, R.245, G.247, R.248, R.484 22 PLIP interactions: 16 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:H.154, A:G.192, A:R.194, A:R.197, A:N.482, A:R.542, A:R.542, A:R.556, A:W.558, D:D.244, D:R.484, D:R.484 Water bridges: A:N.482, A:N.482, A:P.544, D:D.244, D:R.245 Salt bridges: A:R.542, A:R.556 pi-Cation interactions: A:R.197, A:R.197 Hydrophobic interactions: D:R.248 NAD.3: 22 residues within 4Å: Chain B: R.165, N.259, T.283, V.286, G.311, A.312, G.313, E.314, A.315, D.345, K.346, V.392, A.393, G.394, A.395, L.398, L.419, S.420, N.421, G.446, G.465, N.467 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:T.283 Hydrogen bonds: B:N.259, B:A.312, B:A.312, B:E.314, B:A.315, B:D.345, B:K.346, B:N.421, B:N.421, B:N.421, B:G.465, B:N.467 Water bridges: B:R.165, B:R.165, B:G.311, B:G.313, B:A.316 Salt bridges: B:R.165, B:R.165 NAD.4: 20 residues within 4Å: Chain B: H.154, K.156, G.192, I.193, R.194, R.197, I.479, L.480, N.482, R.542, P.544, Y.552, R.556, W.558 Chain C: T.243, D.244, G.247, R.248, N.249, R.484 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:H.154, B:G.192, B:R.194, B:R.197, B:N.482, B:R.542, B:R.542, B:Y.552, B:W.558, C:D.244, C:R.245 Water bridges: B:K.156, B:N.482, B:P.544, B:R.556, B:R.556 Salt bridges: B:R.542, B:R.556 pi-Cation interactions: B:R.197, B:R.197 NAD.5: 23 residues within 4Å: Chain C: R.165, N.259, T.283, L.310, G.311, A.312, G.313, E.314, A.315, F.344, D.345, K.346, V.392, A.393, G.394, A.395, L.398, L.419, S.420, N.421, G.446, G.465, N.467 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:T.283 Hydrogen bonds: C:N.259, C:A.312, C:A.312, C:G.313, C:E.314, C:E.314, C:A.315, C:K.346, C:N.421, C:N.421, C:N.421, C:G.465 Water bridges: C:R.165, C:R.165, C:G.313, C:A.316, C:D.345, C:N.467 Salt bridges: C:R.165, C:R.165 NAD.6: 19 residues within 4Å: Chain B: T.243, D.244, R.245, G.247, R.248, R.484 Chain C: H.154, K.156, G.192, I.193, R.194, R.197, I.479, L.480, N.482, R.542, Y.552, R.556, W.558 22 PLIP interactions: 16 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:H.154, C:G.192, C:R.194, C:R.197, C:N.482, C:R.542, C:R.542, C:R.556, C:W.558, B:D.244, B:R.484, B:R.484 Water bridges: C:N.482, C:N.482, C:P.544, B:D.244, B:R.245 Salt bridges: C:R.542, C:R.556 pi-Cation interactions: C:R.197, C:R.197 Hydrophobic interactions: B:R.248 NAD.7: 22 residues within 4Å: Chain D: R.165, N.259, T.283, V.286, G.311, A.312, G.313, E.314, A.315, D.345, K.346, V.392, A.393, G.394, A.395, L.398, L.419, S.420, N.421, G.446, G.465, N.467 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:T.283 Hydrogen bonds: D:N.259, D:A.312, D:A.312, D:E.314, D:A.315, D:D.345, D:K.346, D:N.421, D:N.421, D:N.421, D:G.465, D:N.467 Water bridges: D:R.165, D:R.165, D:G.311, D:G.313, D:A.316 Salt bridges: D:R.165, D:R.165 NAD.8: 20 residues within 4Å: Chain A: T.243, D.244, G.247, R.248, N.249, R.484 Chain D: H.154, K.156, G.192, I.193, R.194, R.197, I.479, L.480, N.482, R.542, P.544, Y.552, R.556, W.558 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:H.154, D:G.192, D:R.194, D:R.197, D:N.482, D:R.542, D:R.542, D:Y.552, D:W.558, A:D.244, A:R.245 Water bridges: D:K.156, D:N.482, D:P.544, D:R.556, D:R.556 Salt bridges: D:R.542, D:R.556 pi-Cation interactions: D:R.197, D:R.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y. et al., Crystal structure of human mitochondrial NAD(P)(+)-dependent malic enzyme: a new class of oxidative decarboxylases. Structure (1999)

Release Date

1999-07-05

Peptides

MALIC ENZYME 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

MALIC ENZYME 2

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