SMTL ID : 7bsk.1

Crystal structure of human ME2 R67Q mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 20 residues within 4Å: Chain A: N.241, D.261, T.265, L.292, G.293, A.294, G.295, D.327, K.328, V.374, A.375, G.376, A.377, L.380, L.401, S.402, N.403, P.404, G.447, N.449 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.265 Hydrogen bonds: A:A.294, A:G.295, A:K.328, A:N.403, A:N.403 Water bridges: A:N.449 NAD.2: 13 residues within 4Å: Chain A: K.138, G.174, I.175, R.176, R.179, I.461, L.462, N.464, R.524, Y.534, E.537, R.538, W.540 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.176, A:N.464, A:E.537, A:R.538, A:R.538, A:W.540 Salt bridges: A:R.524, A:R.538 pi-Cation interactions: A:R.179, A:R.179 NAD.3: 19 residues within 4Å: Chain B: R.147, L.149, N.241, F.245, L.292, G.293, A.294, G.295, E.296, F.326, D.327, K.328, V.374, A.375, A.377, L.380, S.402, N.403, P.404 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.294, B:E.296, B:K.328, B:V.374, B:S.402, B:N.403, B:N.403 NAD.4: 12 residues within 4Å: Chain B: K.138, G.174, I.175, R.176, R.179, I.461, L.462, N.464, R.524, R.538, W.540 Chain C: R.227 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.176, B:R.176, B:R.179, B:N.464, B:R.538, B:W.540 Salt bridges: B:R.524, B:R.538 NAD.5: 20 residues within 4Å: Chain C: N.241, D.261, T.265, L.292, G.293, A.294, G.295, D.327, K.328, V.374, A.375, G.376, A.377, L.380, L.401, S.402, N.403, P.404, G.447, N.449 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:T.265 Hydrogen bonds: C:A.294, C:G.295, C:K.328, C:N.403, C:N.403 Water bridges: C:N.449 NAD.6: 13 residues within 4Å: Chain C: K.138, G.174, I.175, R.176, R.179, I.461, L.462, N.464, R.524, Y.534, E.537, R.538, W.540 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:R.176, C:N.464, C:E.537, C:R.538, C:R.538, C:W.540 Salt bridges: C:R.524, C:R.538 pi-Cation interactions: C:R.179, C:R.179 NAD.7: 19 residues within 4Å: Chain D: R.147, L.149, N.241, F.245, L.292, G.293, A.294, G.295, E.296, F.326, D.327, K.328, V.374, A.375, A.377, L.380, S.402, N.403, P.404 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:A.294, D:E.296, D:K.328, D:V.374, D:S.402, D:N.403, D:N.403 NAD.8: 12 residues within 4Å: Chain A: R.227 Chain D: K.138, G.174, I.175, R.176, R.179, I.461, L.462, N.464, R.524, R.538, W.540 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.176, D:R.176, D:R.179, D:N.464, D:R.538, D:W.540 Salt bridges: D:R.524, D:R.538

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsieh, J.Y. et al., Single nucleotide variants lead to dysregulation of the human mitochondrial NAD(P) + -dependent malic enzyme. Iscience (2021)

Release Date

2021-02-10

Peptides

NAD-dependent malic enzyme, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

NAD-dependent malic enzyme, mitochondrial