SMTL ID : 9ayi.1

Human malic enzyme 2 cofactor complex at 1.89 Angstrom.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 18 residues within 4Å: Chain A: K.139, G.175, I.176, R.177, R.180, I.462, L.463, N.465, R.525, Y.535, R.539, W.541 Chain D: R.127, T.226, D.227, R.228, G.230 Ligands: TLA.19 20 PLIP interactions: 15 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:K.139, A:R.177, A:R.180, A:N.465, A:R.539, A:W.541, D:R.127, D:R.127, D:D.227 Water bridges: A:R.180, A:R.180, A:N.465, A:N.465, A:N.465, D:R.231, D:R.231 Salt bridges: A:R.525, A:R.539 pi-Cation interactions: A:R.180, A:R.180 NAD.5: 22 residues within 4Å: Chain A: R.148, L.150, N.242, D.262, T.266, L.293, G.294, A.295, G.296, E.297, A.298, F.327, D.328, K.329, V.375, A.376, G.377, A.378, L.381, L.402, S.403, N.404 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:T.266 Hydrogen bonds: A:R.148, A:R.148, A:N.242, A:N.242, A:D.262, A:D.262, A:A.295, A:A.295, A:E.297, A:A.298, A:K.329, A:S.403, A:N.404, A:N.404 Water bridges: A:G.296, A:A.299, A:D.328, A:N.450 NAD.9: 22 residues within 4Å: Chain B: L.150, N.242, T.266, L.293, G.294, A.295, G.296, E.297, A.298, F.327, D.328, K.329, V.375, A.376, G.377, A.378, L.381, L.402, S.403, N.404, G.448, N.450 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:T.266 Hydrogen bonds: B:N.242, B:N.242, B:A.295, B:A.295, B:E.297, B:A.298, B:K.329, B:L.402, B:S.403, B:N.404 Water bridges: B:G.151, B:G.296, B:A.299, B:D.328, B:N.450 NAD.12: 19 residues within 4Å: Chain B: K.139, G.175, I.176, R.177, R.180, I.462, L.463, N.465, R.525, Y.535, R.539, W.541 Chain C: N.136, H.137, R.228, Y.229, G.230 Ligands: TLA.14, NAD.17 20 PLIP interactions: 17 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:K.139, B:R.177, B:R.180, B:N.465, B:Y.535, B:R.539, B:W.541, C:H.137 Water bridges: B:R.177, B:R.180, B:N.465, B:N.465, B:R.539, B:R.539, C:R.231, C:R.231 Salt bridges: B:R.525, B:R.539 pi-Cation interactions: B:R.180, B:R.180 NAD.17: 19 residues within 4Å: Chain B: N.136, H.137, R.228, Y.229, G.230 Chain C: K.139, G.175, I.176, R.177, R.180, I.462, L.463, N.465, R.525, Y.535, R.539, W.541 Ligands: TLA.10, NAD.12 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:K.139, C:R.177, C:R.180, C:N.465, C:R.539, C:W.541 Water bridges: C:N.465, C:N.465, C:N.465, B:R.231 Salt bridges: C:R.525, C:R.539 pi-Cation interactions: C:R.180, C:R.180 NAD.18: 23 residues within 4Å: Chain C: L.150, N.242, T.266, L.293, G.294, A.295, G.296, E.297, A.298, F.327, D.328, K.329, V.375, A.376, G.377, A.378, L.381, L.402, S.403, N.404, G.429, G.448, N.450 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:T.266 Hydrogen bonds: C:N.242, C:A.295, C:A.295, C:E.297, C:E.297, C:A.298, C:D.328, C:K.329, C:L.402, C:S.403, C:N.404, C:N.404 Water bridges: C:R.148, C:G.296, C:A.299, C:N.450 NAD.21: 21 residues within 4Å: Chain D: L.150, N.242, T.266, G.294, A.295, G.296, E.297, A.298, D.328, K.329, V.375, A.376, G.377, A.378, L.381, L.402, S.403, N.404, G.429, G.448, N.450 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:T.266 Hydrogen bonds: D:R.148, D:N.242, D:A.295, D:E.297, D:A.298, D:K.329, D:L.402, D:S.403, D:N.404, D:N.404, D:N.404 Water bridges: D:G.296, D:E.297, D:A.299, D:N.450 NAD.23: 18 residues within 4Å: Chain A: N.136, H.137, R.228, Y.229, G.230 Chain D: K.139, G.175, I.176, R.177, R.180, I.462, L.463, N.465, R.525, Y.535, R.539, W.541 Ligands: TLA.7 14 PLIP interactions: 1 interactions with chain A, 13 interactions with chain D Water bridges: A:R.231, D:R.180, D:N.465, D:N.465 Hydrogen bonds: D:K.139, D:R.177, D:R.180, D:N.465, D:R.539, D:W.541 Salt bridges: D:R.525, D:R.539 pi-Cation interactions: D:R.180, D:R.180

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: Q.84, Q.503, W.541, R.542, S.543 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.84, A:Q.503, A:S.543 Water bridges: A:S.543 EDO.3: 4 residues within 4Å: Chain A: I.285, H.288, I.290, S.309 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.309, A:S.309 EDO.11: 4 residues within 4Å: Chain B: L.274, Q.278, H.288, I.290 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.274 EDO.15: 5 residues within 4Å: Chain C: L.271, Q.278, H.288, I.306, M.310 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.278 EDO.22: 6 residues within 4Å: Chain D: L.274, A.277, Q.278, H.288, I.290, T.371 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.274, D:T.371 Water bridges: D:T.371

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 5 residues within 4Å: Chain A: G.20, M.21, Q.47 Chain B: I.109, F.110 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain A: I.109, F.110 Chain B: G.20, M.21, Q.47 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain C: G.20, M.21, Q.47 Chain D: F.110 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain C: I.109, F.110 Chain D: G.20, M.21, Q.47 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: H.137 Chain D: H.137 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: D:H.137, A:H.137, H2O.15, H2O.69, H2O.72 MG.13: 2 residues within 4Å: Chain B: H.137 Chain C: H.137 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:H.137, B:H.137, H2O.34, H2O.37, H2O.57

4 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.7: 6 residues within 4Å: Chain A: G.230, R.231, R.467 Chain D: R.525, P.527 Ligands: NAD.23 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:R.231, D:R.525 Water bridges: A:N.232, D:R.525 Salt bridges: A:R.467, D:R.525 TLA.10: 6 residues within 4Å: Chain B: G.230, R.231, R.467 Chain C: R.525, P.527 Ligands: NAD.17 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:R.231, B:R.467, B:R.467, C:R.525, C:R.525 Water bridges: B:N.232, C:R.539, C:R.539 Salt bridges: B:R.467, B:R.467, C:R.525, C:R.525 TLA.14: 6 residues within 4Å: Chain B: R.525, P.527 Chain C: G.230, R.231, R.467 Ligands: NAD.12 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:R.231, C:R.467, C:R.467, B:R.525, B:R.525 Water bridges: C:N.232, C:N.232, B:R.539, B:R.539 Salt bridges: C:R.467, C:R.467, B:R.525 TLA.19: 6 residues within 4Å: Chain A: R.525, P.527 Chain D: G.230, R.231, R.467 Ligands: NAD.1 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:R.231, D:R.467, D:R.467, A:R.525, A:R.525 Water bridges: D:N.232, D:N.232, D:N.232 Salt bridges: D:R.467, D:R.467, A:R.525

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krinkel, B.A. et al., Human malic enzyme 2 complex with inhibitor NPD-389. To Be Published

Release Date

2025-03-12

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