SMTL ID : 7xdf.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Covalent)

NAD.1: 19 residues within 4Å: Chain A: F.263, D.279, 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, S.420, N.421 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:D.279, A:T.283, A:A.315 Hydrogen bonds: A:A.312, A:E.314, A:A.315, A:D.345, A:K.346, A:K.346, A:N.421, A:N.421, A:N.421, A:N.421 NAD.2: 12 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, 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:N.482, A:Y.552, A:R.556, A:W.558 Salt bridges: A:R.542, A:R.556 NAD.4: 19 residues within 4Å: Chain B: F.263, D.279, 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, S.420, N.421 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:D.279, B:T.283, B:A.315 Hydrogen bonds: B:A.312, B:E.314, B:A.315, B:D.345, B:K.346, B:K.346, B:N.421, B:N.421, B:N.421, B:N.421 NAD.5: 12 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, 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:N.482, B:Y.552, B:R.556, B:W.558 Salt bridges: B:R.542, B:R.556 NAD.7: 19 residues within 4Å: Chain C: F.263, D.279, 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, S.420, N.421 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:D.279, C:T.283, C:A.315 Hydrogen bonds: C:T.283, C:A.312, C:E.314, C:A.315, C:K.346, C:K.346, C:N.421, C:N.421, C:N.421, C:N.421 NAD.8: 12 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, 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:N.482, C:R.556, C:W.558 Salt bridges: C:R.542, C:R.556 NAD.10: 19 residues within 4Å: Chain D: F.263, D.279, 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, S.420, N.421 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:D.279, D:T.283, D:A.315 Hydrogen bonds: D:T.283, D:A.312, D:E.314, D:A.315, D:K.346, D:K.346, D:N.421, D:N.421, D:N.421, D:N.421 NAD.11: 12 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, 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:N.482, D:R.556, D:W.558 Salt bridges: D:R.542, D:R.556

4 x JBR: 4-[(3-carboxy-2-oxidanyl-naphthalen-1-yl)methyl]-3-oxidanyl-naphthalene-2-carboxylic acid(Non-covalent)

JBR.3: 15 residues within 4Å: Chain A: N.35, G.37, M.38, P.55, Q.64, R.67, F.68, Y.84, R.91, N.92, L.95 Chain B: H.125, Y.175, F.217, M.219 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.55, B:Y.175, B:M.219 Hydrogen bonds: A:N.35, A:Q.64, A:Y.84, A:N.92 Salt bridges: A:R.91, A:R.91 pi-Cation interactions: A:R.91 JBR.6: 15 residues within 4Å: Chain A: H.125, Y.175, F.217, M.219 Chain B: N.35, G.37, M.38, P.55, Q.64, R.67, F.68, Y.84, R.91, N.92, L.95 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.55, A:Y.175, A:M.219 Hydrogen bonds: B:N.35, B:Q.64, B:Y.84, B:N.92 Salt bridges: B:R.91, B:R.91 pi-Cation interactions: B:R.91 JBR.9: 14 residues within 4Å: Chain C: N.35, G.37, M.38, P.55, R.67, F.68, Y.84, R.91, N.92, L.95 Chain D: H.125, Y.175, F.217, M.219 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:P.55, D:Y.175, D:M.219 Hydrogen bonds: C:N.35, C:Q.64, C:N.92 Salt bridges: C:R.91, C:R.91 pi-Cation interactions: C:R.91 JBR.12: 14 residues within 4Å: Chain C: H.125, Y.175, F.217, M.219 Chain D: N.35, G.37, M.38, P.55, R.67, F.68, Y.84, R.91, N.92, L.95 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:Y.175, C:M.219, D:P.55 Hydrogen bonds: D:N.35, D:Q.64, D:N.92 Salt bridges: D:R.91, D:R.91 pi-Cation interactions: 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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