SMTL ID : 7sni.1

Structure of G6PD-D200N tetramer bound to NADP+ and G6P

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 16 residues within 4Å: Chain A: S.40, G.41, D.42, L.43, A.71, R.72, S.73, Y.112, A.141, L.142, P.143, P.144, V.146, E.170, K.171, P.172 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.43 Hydrogen bonds: A:S.40, A:S.40, A:S.40, A:D.42, A:D.42, A:L.43, A:R.72, A:R.72, A:S.73, A:Y.112, A:L.142, A:Y.147 Water bridges: A:A.44 Salt bridges: A:R.72 pi-Cation interactions: A:R.72 NAP.2: 19 residues within 4Å: Chain A: K.238, R.357, E.364, K.366, E.368, R.370, R.393, A.399, Y.401, K.403, D.421, T.423, R.487, D.493, M.496, F.501, Y.503, Y.507, W.509 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:R.357, A:E.364, A:K.366, A:E.368, A:R.370, A:R.370, A:R.393, A:R.393, A:T.423, A:T.423, A:R.487, A:R.487 Water bridges: A:K.238, A:K.403 Salt bridges: A:K.238, A:R.357, A:K.366, A:R.370, A:R.370, A:K.403, A:K.403, A:R.487 pi-Stacking: A:Y.401, A:Y.503, A:Y.503, A:W.509, A:W.509 pi-Cation interactions: A:R.487 NAP.4: 16 residues within 4Å: Chain B: S.40, G.41, D.42, L.43, A.71, R.72, S.73, Y.112, A.141, L.142, P.143, P.144, V.146, E.170, K.171, P.172 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.43 Hydrogen bonds: B:S.40, B:S.40, B:S.40, B:D.42, B:D.42, B:L.43, B:R.72, B:R.72, B:S.73, B:Y.112, B:L.142 Water bridges: B:A.44 Salt bridges: B:R.72 pi-Cation interactions: B:R.72 NAP.5: 19 residues within 4Å: Chain B: K.238, R.357, E.364, K.366, E.368, R.370, R.393, A.399, Y.401, K.403, D.421, T.423, R.487, D.493, M.496, F.501, Y.503, Y.507, W.509 29 PLIP interactions: 29 interactions with chain B Hydrogen bonds: B:R.357, B:E.364, B:K.366, B:E.368, B:R.370, B:R.370, B:R.393, B:R.393, B:T.423, B:T.423, B:R.487, B:R.487, B:D.493 Water bridges: B:K.238, B:K.403 Salt bridges: B:K.238, B:R.357, B:K.366, B:R.370, B:R.370, B:K.403, B:K.403, B:R.487 pi-Stacking: B:Y.401, B:Y.503, B:Y.503, B:W.509, B:W.509 pi-Cation interactions: B:R.487 NAP.7: 16 residues within 4Å: Chain C: S.40, G.41, D.42, L.43, A.71, R.72, S.73, Y.112, A.141, L.142, P.143, P.144, V.146, E.170, K.171, P.172 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.43 Hydrogen bonds: C:S.40, C:S.40, C:S.40, C:D.42, C:L.43, C:R.72, C:R.72, C:S.73, C:L.142 Water bridges: C:A.44 Salt bridges: C:R.72 pi-Cation interactions: C:R.72 NAP.8: 19 residues within 4Å: Chain C: K.238, R.357, E.364, K.366, E.368, R.370, R.393, A.399, Y.401, K.403, D.421, T.423, R.487, D.493, M.496, F.501, Y.503, Y.507, W.509 26 PLIP interactions: 26 interactions with chain C Hydrogen bonds: C:R.357, C:K.366, C:R.370, C:R.370, C:R.393, C:R.393, C:Y.401, C:T.423, C:R.487, C:R.487 Water bridges: C:K.238, C:K.403 Salt bridges: C:K.238, C:R.357, C:K.366, C:R.370, C:R.370, C:K.403, C:K.403, C:R.487 pi-Stacking: C:Y.401, C:Y.503, C:Y.503, C:W.509, C:W.509 pi-Cation interactions: C:R.487 NAP.10: 16 residues within 4Å: Chain D: S.40, G.41, D.42, L.43, A.71, R.72, S.73, Y.112, A.141, L.142, P.143, P.144, V.146, E.170, K.171, P.172 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:L.43 Hydrogen bonds: D:S.40, D:S.40, D:S.40, D:D.42, D:L.43, D:R.72, D:R.72, D:S.73, D:L.142 Water bridges: D:A.44 Salt bridges: D:R.72 pi-Cation interactions: D:R.72 NAP.11: 19 residues within 4Å: Chain D: K.238, R.357, E.364, K.366, E.368, R.370, R.393, A.399, Y.401, K.403, D.421, T.423, R.487, D.493, M.496, F.501, Y.503, Y.507, W.509 26 PLIP interactions: 26 interactions with chain D Hydrogen bonds: D:R.357, D:K.366, D:R.370, D:R.370, D:R.393, D:R.393, D:Y.401, D:T.423, D:R.487, D:R.487 Water bridges: D:K.238, D:K.403 Salt bridges: D:K.238, D:R.357, D:K.366, D:R.370, D:R.370, D:K.403, D:K.403, D:R.487 pi-Stacking: D:Y.401, D:Y.503, D:Y.503, D:W.509, D:W.509 pi-Cation interactions: D:R.487

4 x BG6: 6-O-phosphono-beta-D-glucopyranose(Non-covalent)

BG6.3: 11 residues within 4Å: Chain A: K.171, H.201, Y.202, K.205, F.237, E.239, D.258, H.263, K.360, R.365, Q.395 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:K.171, A:K.171, A:Y.202, A:D.258, A:K.360, A:K.360, A:Q.395 Salt bridges: A:K.171, A:H.201, A:H.201, A:K.205, A:H.263, A:R.365 BG6.6: 11 residues within 4Å: Chain B: K.171, H.201, Y.202, K.205, F.237, E.239, D.258, H.263, K.360, R.365, Q.395 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:K.171, B:K.171, B:Y.202, B:D.258, B:K.360, B:K.360, B:Q.395 Salt bridges: B:K.171, B:H.201, B:H.201, B:K.205, B:H.263, B:R.365 BG6.9: 11 residues within 4Å: Chain C: K.171, H.201, Y.202, K.205, F.237, E.239, D.258, H.263, K.360, R.365, Q.395 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:K.171, C:K.171, C:D.258, C:K.360, C:K.360, C:Q.395 Salt bridges: C:K.171, C:H.201, C:H.201, C:K.205, C:H.263, C:R.365 BG6.12: 11 residues within 4Å: Chain D: K.171, H.201, Y.202, K.205, F.237, E.239, D.258, H.263, K.360, R.365, Q.395 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:K.171, D:K.171, D:D.258, D:K.360, D:K.360, D:Q.395 Salt bridges: D:K.171, D:H.201, D:H.201, D:K.205, D:H.263, D:R.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, X. et al., Allosteric role of a structural NADP + molecule in glucose-6-phosphate dehydrogenase activity. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-07-13

Peptides

Glucose-6-phosphate 1-dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glucose-6-phosphate 1-dehydrogenase

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