SMTL ID : 7x12.1

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 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.245, A:D.246, A:D.269, H2O.1, H2O.2, H2O.2 MN.3: 3 residues within 4Å: Chain B: E.245, D.246, D.269 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.245, B:D.246, B:D.269, H2O.4, H2O.6, H2O.8 MN.5: 3 residues within 4Å: Chain C: E.245, D.246, D.269 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.245, C:D.246, C:D.269, H2O.10, H2O.12, H2O.12 MN.7: 3 residues within 4Å: Chain D: E.245, D.246, D.269 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.245, D:D.246, D:D.269, H2O.15, H2O.18, H2O.19

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

NDP.2: 24 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 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:T.273, A:A.305 Hydrogen bonds: A:N.249, A:N.249, A:Q.300, 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:G.303, A:A.306, A:K.351, A:K.351, A:N.454, A:N.454 Salt bridges: A:R.155, A:K.337, A:K.351 NDP.4: 23 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 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:T.273 Hydrogen bonds: B:N.249, B:Q.300, 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:G.303, B:A.306, B:K.351, B:K.351 Salt bridges: B:R.155, B:K.351 NDP.6: 23 residues within 4Å: Chain C: R.155, 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 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:T.273, C:A.305 Hydrogen bonds: 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:G.452 Water bridges: C:G.303, C:G.303 Salt bridges: C:R.155, C:R.155, C:K.337, C:K.351 NDP.8: 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 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:T.273, D:A.305 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:G.452 Water bridges: D:G.303, D:K.351, D:K.351, D:N.454 Salt bridges: D:R.155, D:K.351

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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