SMTL ID : 7bsj.1

Crystal structure of human ME2 R484W

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 28 residues within 4Å: Chain A: R.147, L.149, G.150, N.241, D.261, T.265, L.292, G.293, A.294, G.295, E.296, A.297, F.326, D.327, K.328, V.374, A.375, G.376, A.377, L.380, L.401, S.402, N.403, G.428, G.447, N.448, N.449 Ligands: TTN.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.265 Hydrogen bonds: A:L.149, A:N.241, A:T.265, A:A.294, A:E.296, A:E.296, A:A.297, A:K.328, A:L.401, A:N.403, A:N.403, A:N.449 Salt bridges: A:R.147 NAD.3: 14 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 Chain D: R.230 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.176, A:R.179, A:R.179, A:N.464, A:R.538, A:W.540 Salt bridges: A:R.524, A:R.538, D:R.230, D:R.230 NAD.6: 28 residues within 4Å: Chain B: R.147, L.149, G.150, N.241, D.261, T.265, L.292, G.293, A.294, G.295, E.296, A.297, F.326, D.327, K.328, V.374, A.375, G.376, A.377, L.380, L.401, S.402, N.403, G.428, G.447, N.448, N.449 Ligands: TTN.10 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:T.265 Hydrogen bonds: B:R.147, B:L.149, B:N.241, B:A.294, B:A.294, B:E.296, B:A.297, B:K.328, B:L.401, B:S.402, B:N.403, B:N.403, B:N.448, B:N.449 Salt bridges: B:R.147 NAD.8: 18 residues within 4Å: Chain B: H.136, K.138, G.174, I.175, R.176, I.461, L.462, N.464, R.524, Y.534, R.538, W.540 Chain C: N.135, H.136, D.226, R.227, Y.228, G.229 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:H.136, B:K.138, B:G.174, B:R.176, B:R.179, B:N.464, B:Y.534, B:Y.534, B:W.540, C:Y.228 Salt bridges: B:R.524, B:R.538 pi-Stacking: B:H.136 pi-Cation interactions: B:R.179 NAD.11: 28 residues within 4Å: Chain C: R.147, L.149, G.150, N.241, D.261, T.265, L.292, G.293, A.294, G.295, E.296, A.297, F.326, D.327, K.328, V.374, A.375, G.376, A.377, L.380, L.401, S.402, N.403, G.428, G.447, N.448, N.449 Ligands: TTN.15 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:T.265 Hydrogen bonds: C:L.149, C:N.241, C:A.294, C:E.296, C:A.297, C:K.328, C:L.401, C:N.403, C:N.403, C:N.449 Salt bridges: C:R.147 NAD.13: 14 residues within 4Å: Chain B: R.230 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 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.176, C:R.179, C:R.179, C:N.464, C:Y.534, C:R.538, C:W.540 Salt bridges: C:R.524, C:R.538, B:R.230, B:R.230 NAD.16: 28 residues within 4Å: Chain D: R.147, L.149, G.150, N.241, D.261, T.265, L.292, G.293, A.294, G.295, E.296, A.297, F.326, D.327, K.328, V.374, A.375, G.376, A.377, L.380, L.401, S.402, N.403, G.428, G.447, N.448, N.449 Ligands: TTN.20 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:T.265 Hydrogen bonds: D:R.147, D:L.149, D:N.241, D:A.294, D:A.294, D:E.296, D:E.296, D:A.297, D:K.328, D:L.401, D:S.402, D:N.403, D:N.403, D:N.448, D:N.449 Salt bridges: D:R.147 NAD.18: 18 residues within 4Å: Chain A: N.135, H.136, D.226, R.227, Y.228, G.229 Chain D: H.136, K.138, G.174, I.175, R.176, I.461, L.462, N.464, R.524, Y.534, R.538, W.540 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:K.138, D:G.174, D:R.176, D:R.179, D:N.464, D:Y.534, D:W.540, A:Y.228 Salt bridges: D:R.524, D:R.538 pi-Stacking: D:H.136 pi-Cation interactions: D:R.179

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: R.147, E.237, D.238, D.261 Ligands: TTN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.237, A:D.238, A:D.238, A:D.261 MG.7: 6 residues within 4Å: Chain B: R.147, K.165, E.237, D.238, D.261 Ligands: TTN.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.237, B:D.238, B:D.261 MG.12: 5 residues within 4Å: Chain C: R.147, E.237, D.238, D.261 Ligands: TTN.15 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.237, C:D.238, C:D.238, C:D.261 MG.17: 6 residues within 4Å: Chain D: R.147, K.165, E.237, D.238, D.261 Ligands: TTN.20 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.237, D:D.238, D:D.261

4 x FUM: FUMARIC ACID(Non-covalent)

FUM.4: 7 residues within 4Å: Chain A: Q.46, R.49, I.70, R.73, L.77 Chain B: F.109, R.110 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.77 Hydrogen bonds: A:Q.46 Water bridges: A:R.49, A:R.49, A:N.74 Salt bridges: A:R.49, A:R.73 FUM.9: 7 residues within 4Å: Chain A: F.109, R.110 Chain B: Q.46, R.49, I.70, R.73, L.77 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.77 Hydrogen bonds: B:Q.46 Water bridges: B:Q.46, B:Y.66 Salt bridges: B:R.49, B:R.73 FUM.14: 7 residues within 4Å: Chain C: Q.46, R.49, I.70, R.73, L.77 Chain D: F.109, R.110 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.77 Hydrogen bonds: C:Q.46 Water bridges: C:E.41, C:R.49, C:N.74 Salt bridges: C:R.49, C:R.73 FUM.19: 7 residues within 4Å: Chain C: F.109, R.110 Chain D: Q.46, R.49, I.70, R.73, L.77 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.77 Hydrogen bonds: D:Q.46 Water bridges: D:Q.46, D:Y.66 Salt bridges: D:R.49, D:R.73

4 x TTN: TARTRONATE(Non-covalent)

TTN.5: 12 residues within 4Å: Chain A: Y.94, R.147, L.149, K.165, E.237, D.238, D.261, N.403, N.448, N.449 Ligands: NAD.1, MG.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.165, A:D.261, A:N.403, A:N.448, A:N.449 Salt bridges: A:R.147, A:K.165 TTN.10: 12 residues within 4Å: Chain B: Y.94, R.147, L.149, K.165, E.237, D.238, D.261, N.403, N.448, N.449 Ligands: NAD.6, MG.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.94, B:K.165, B:N.403, B:N.448, B:N.449 Salt bridges: B:R.147, B:K.165 TTN.15: 12 residues within 4Å: Chain C: Y.94, R.147, L.149, K.165, E.237, D.238, D.261, N.403, N.448, N.449 Ligands: NAD.11, MG.12 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.94, C:K.165, C:N.403, C:N.448, C:N.449 Salt bridges: C:R.147, C:K.165 TTN.20: 12 residues within 4Å: Chain D: Y.94, R.147, L.149, K.165, E.237, D.238, D.261, N.403, N.448, N.449 Ligands: NAD.16, MG.17 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.165, D:N.403, D:N.448, D:N.449 Salt bridges: D:R.147, D:K.165

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