SMTL ID : 6e07.2 (3 other biounits)

Crystal structure of Canton G6PD in complex with structural NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 18 residues within 4Å: Chain A: K.238, R.357, E.364, K.366, 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 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.393, A:R.393, A:Y.401, A:D.421, A:R.487 Water bridges: A:R.393 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.8: 16 residues within 4Å: Chain B: K.238, E.364, K.366, R.370, R.393, A.399, Y.401, K.403, D.421, T.423, R.487, D.493, F.501, Y.503, Y.507, W.509 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:R.370, B:R.393, B:R.393, B:T.423, B:R.487 Water bridges: B:K.403, B:D.493, B:D.493, B:Y.503, B:Y.503 Salt bridges: B:K.238, 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

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: H.201, Y.202, K.205, R.365, Q.395 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.202, A:R.365, A:Q.395 Salt bridges: A:H.201, A:K.205 PO4.9: 3 residues within 4Å: Chain B: H.201, K.205, R.365 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.365 Salt bridges: B:H.201, B:K.205

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: R.227, D.350 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.227, A:R.227, A:D.350 GOL.4: 2 residues within 4Å: Chain A: Y.343, E.345 No protein-ligand interaction detected (PLIP) GOL.5: 4 residues within 4Å: Chain A: E.491, E.494, L.495, R.498 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.494, A:E.494, A:R.498 GOL.6: 2 residues within 4Å: Chain A: Q.471, E.475 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.471, A:E.475 GOL.7: 3 residues within 4Å: Chain A: R.120, S.123, H.124 No protein-ligand interaction detected (PLIP) GOL.10: 1 residues within 4Å: Chain B: R.227 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.227, B:R.227 GOL.11: 2 residues within 4Å: Chain B: Y.343, E.345 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.345, B:E.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hwang, S. et al., Correcting glucose-6-phosphate dehydrogenase deficiency with a small-molecule activator. Nat Commun (2018)

Release Date

2018-07-25

Peptides

Glucose-6-phosphate 1-dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
W

Glucose-6-phosphate 1-dehydrogenase

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