SMTL ID : 7xdg.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

NAD.1: 18 residues within 4Å: Chain A: N.259, F.263, D.279, T.283, L.310, G.311, A.312, G.313, A.315, F.344, D.345, K.346, V.392, A.393, G.394, A.395, L.398, S.420 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.283, A:A.315 Hydrogen bonds: A:N.259, A:D.279, A:D.279, A:A.312, A:A.312, A:A.315, A:K.346, A:K.346, A:K.346, A:A.393 NAD.2: 13 residues within 4Å: Chain A: K.156, G.192, I.193, R.194, R.197, I.479, L.480, N.482, R.542, Y.552, R.556, T.557, W.558 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.156, A:R.194, A:R.194, A:R.194, A:R.197, A:R.197, A:N.482, A:Y.552, A:R.556 Salt bridges: A:R.542, A:R.556 NAD.4: 18 residues within 4Å: Chain B: N.259, F.263, D.279, T.283, L.310, G.311, A.312, G.313, A.315, F.344, D.345, K.346, V.392, A.393, G.394, A.395, L.398, S.420 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.283, B:A.315 Hydrogen bonds: B:N.259, B:D.279, B:D.279, B:A.312, B:A.312, B:A.315, B:K.346, B:K.346, B:K.346, B:A.393 NAD.5: 13 residues within 4Å: Chain B: K.156, G.192, I.193, R.194, R.197, I.479, L.480, N.482, R.542, Y.552, R.556, T.557, W.558 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.156, B:R.194, B:R.194, B:R.194, B:R.197, B:R.197, B:N.482, B:Y.552, B:R.556 Salt bridges: B:R.542, B:R.556 NAD.7: 18 residues within 4Å: Chain C: N.259, F.263, D.279, T.283, L.310, G.311, A.312, G.313, A.315, F.344, D.345, K.346, V.392, A.393, G.394, A.395, L.398, S.420 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:T.283, C:A.315 Hydrogen bonds: C:N.259, C:D.279, C:A.312, C:A.312, C:A.315, C:D.345, C:K.346, C:K.346, C:K.346, C:A.393 NAD.8: 13 residues within 4Å: Chain C: K.156, G.192, I.193, R.194, R.197, I.479, L.480, N.482, R.542, Y.552, R.556, T.557, W.558 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:K.156, C:R.194, C:R.194, C:R.194, C:R.197, C:R.197, C:N.482, C:R.556 Salt bridges: C:R.542, C:R.556 NAD.10: 18 residues within 4Å: Chain D: N.259, F.263, D.279, T.283, L.310, G.311, A.312, G.313, A.315, F.344, D.345, K.346, V.392, A.393, G.394, A.395, L.398, S.420 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:T.283, D:A.315 Hydrogen bonds: D:N.259, D:D.279, D:A.312, D:A.312, D:A.315, D:D.345, D:K.346, D:K.346, D:K.346, D:A.393 NAD.11: 13 residues within 4Å: Chain D: K.156, G.192, I.193, R.194, R.197, I.479, L.480, N.482, R.542, Y.552, R.556, T.557, W.558 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:K.156, D:R.194, D:R.194, D:R.194, D:R.197, D:R.197, D:N.482, D:R.556 Salt bridges: D:R.542, D:R.556

4 x D5S: 5-[(3-carboxy-4-oxidanyl-phenyl)methyl]-2-oxidanyl-benzoic acid(Non-covalent)

D5S.3: 10 residues within 4Å: Chain A: G.37, M.38, E.59, Q.64, R.67, F.68, Y.84, R.91 Chain B: H.125, R.128 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.68, A:F.68, A:Y.84 Hydrogen bonds: A:M.38, A:Q.64, B:R.128 Salt bridges: A:R.67, A:R.91 D5S.6: 10 residues within 4Å: Chain A: H.125, R.128 Chain B: G.37, M.38, E.59, Q.64, R.67, F.68, Y.84, R.91 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:R.128, B:M.38, B:Q.64 Hydrophobic interactions: B:F.68, B:F.68, B:Y.84 Salt bridges: B:R.67, B:R.91 D5S.9: 10 residues within 4Å: Chain C: G.37, M.38, E.59, Q.64, R.67, F.68, Y.84, R.91 Chain D: H.125, R.128 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.68, C:F.68, C:Y.84 Hydrogen bonds: C:M.38, C:Q.64, D:R.128 Salt bridges: C:R.67, C:R.91 D5S.12: 10 residues within 4Å: Chain C: H.125, R.128 Chain D: G.37, M.38, E.59, Q.64, R.67, F.68, Y.84, R.91 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.68, D:F.68, D:Y.84 Hydrogen bonds: D:M.38, D:Q.64, C:R.128 Salt bridges: D:R.67, D:R.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsieh, J.Y. et al., Suppression of the human malic enzyme 2 modifies energy metabolism and inhibits cellular respiration. Commun Biol (2023)

Release Date

2023-03-29

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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