SMTL ID : 7x11.1

Crystal structure of ME1 in complex with NADPH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-tetramer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 3 residues within 4Å: Chain A: E.245, D.246, D.269 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.245, A:D.246, A:D.269, H2O.5 MN.4: 3 residues within 4Å: Chain B: E.245, D.246, D.269 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.245, B:D.246, B:D.269, H2O.11, H2O.13 MN.7: 3 residues within 4Å: Chain C: E.245, D.246, D.269 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.245, C:D.269, H2O.15, H2O.16, H2O.16 MN.10: 3 residues within 4Å: Chain D: E.245, D.246, D.269 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.245, D:D.246, D:D.269, H2O.19, H2O.22

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.2: 25 residues within 4Å: Chain A: R.155, N.249, T.273, Q.300, G.301, A.302, G.303, E.304, A.305, V.334, D.335, S.336, K.337, K.351, V.379, A.380, A.381, I.382, L.406, S.407, N.408, G.433, G.452, N.454 Ligands: 86I.3 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:T.273 Hydrogen bonds: A:N.249, A:Q.300, A:G.301, A:A.302, A:A.302, A:E.304, A:A.305, A:D.335, A:S.336, A:S.336, A:N.408, A:N.408, A:G.452 Water bridges: A:E.304, A:K.337, A:K.351, A:K.351, A:N.454 Salt bridges: A:R.155, A:K.337, A:K.351 NDP.5: 24 residues within 4Å: Chain B: R.155, N.249, T.273, Q.300, G.301, A.302, G.303, E.304, A.305, V.334, D.335, S.336, K.351, V.379, A.380, A.381, I.382, L.406, S.407, N.408, G.433, G.452, N.454 Ligands: 86I.6 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:T.273 Hydrogen bonds: B:N.249, B:Q.300, B:G.301, B:A.302, B:A.302, B:E.304, B:E.304, B:A.305, B:D.335, B:S.336, B:S.336, B:N.408, B:N.408, B:N.408, B:G.452 Water bridges: B:Q.300, B:K.351, B:K.351 Salt bridges: B:R.155, B:K.351 NDP.8: 24 residues within 4Å: Chain C: R.155, N.249, T.273, Q.300, G.301, A.302, G.303, E.304, A.305, V.334, D.335, S.336, K.337, K.351, V.379, A.380, A.381, I.382, L.406, S.407, N.408, G.433, G.452, N.454 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:T.273 Hydrogen bonds: C:N.249, C:Q.300, C:A.302, C:A.302, C:E.304, C:A.305, C:D.335, C:S.336, C:N.408, C:N.408, C:N.408, C:G.452 Water bridges: C:N.454 Salt bridges: C:R.155, C:K.337, C:K.351 NDP.11: 23 residues within 4Å: Chain D: R.155, N.249, T.273, Q.300, G.301, A.302, G.303, E.304, A.305, V.334, D.335, S.336, K.351, V.379, A.380, A.381, I.382, L.406, S.407, N.408, G.433, G.452, N.454 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:T.273 Hydrogen bonds: D:N.249, D:Q.300, D:A.302, D:A.302, D:E.304, D:E.304, D:A.305, D:D.335, D:S.336, D:N.408, D:N.408, D:N.408, D:G.452 Water bridges: D:R.155, D:R.155, D:G.303 Salt bridges: D:R.155, D:K.351

4 x 86I: 6-[(7-methyl-2-propyl-imidazo[4,5-b]pyridin-4-yl)methyl]-2-[2-(1H-1,2,3,4-tetrazol-5-yl)phenyl]-1,3-benzothiazole(Non-covalent)

86I.3: 13 residues within 4Å: Chain A: N.249, F.253, R.260, I.270, Q.271, G.303, E.304, L.307, G.308, H.311, E.350, D.475 Ligands: NDP.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:N.249, A:F.253, A:I.270, A:I.270, A:L.307, A:D.475 Hydrogen bonds: A:R.260 Water bridges: A:T.348, A:T.348 pi-Stacking: A:F.253, A:H.311, A:H.311 86I.6: 10 residues within 4Å: Chain B: N.249, F.253, E.304, L.307, G.308, H.311, E.350, K.353, D.475 Ligands: NDP.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:N.249, B:L.307, B:E.350 pi-Stacking: B:F.253, B:F.253, B:H.311, B:H.311 86I.9: 11 residues within 4Å: Chain C: N.249, F.253, R.260, Q.271, A.274, E.304, L.307, G.308, H.311, E.350, D.475 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:N.249, C:F.253, C:F.253, C:Q.271, C:A.274, C:L.307, C:E.350 Hydrogen bonds: C:R.260 pi-Stacking: C:F.253, C:H.311, C:H.311 86I.12: 15 residues within 4Å: Chain D: N.249, V.250, F.253, R.260, I.270, Q.271, A.274, G.303, E.304, L.307, G.308, H.311, L.312, E.350, D.475 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:N.249, D:V.250, D:F.253, D:I.270, D:Q.271, D:A.274, D:L.307, D:L.312, D:E.350 Hydrogen bonds: D:R.260 pi-Stacking: D:F.253, D:F.253, D:H.311, D:H.311

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshida, T. et al., Discovery and Characterization of a Novel Allosteric Small-Molecule Inhibitor of NADP + -Dependent Malic Enzyme 1. Biochemistry (2022)

Release Date

2022-07-20

Peptides

NADP-dependent malic enzyme: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NADP-dependent malic enzyme

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