SMTL ID : 6e07.1 (3 other biounits)

Crystal structure of Canton G6PD in complex with structural NADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 16 residues within 4Å: Chain A: K.238, R.357, E.364, K.366, R.370, R.393, Y.401, K.403, D.421, T.423, R.487, D.493, F.501, Y.503, Y.507, W.509 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:R.370, A:R.393, A:R.393, A:Y.401, A:D.421, A:R.487 Water bridges: A:K.238, A:K.238, A:D.493, A:W.509 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.10: 17 residues within 4Å: Chain B: K.238, E.364, K.366, R.370, R.393, Y.401, K.403, D.421, T.423, R.487, D.493, M.496, F.501, Y.503, Y.507, W.509 Ligands: GOL.14 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:R.370, B:R.393, B:R.393, B:D.421, B:R.487 Water bridges: B:K.238, B:K.238, B:R.357, B:R.487, 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 PO4.11: 5 residues within 4Å: Chain B: H.201, Y.202, K.205, R.365, Q.395 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.202, B:R.365, B:Q.395, B:Q.395 Water bridges: B:K.205 Salt bridges: B:H.201, B:K.205

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: R.227, D.350 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.227, A:R.227 GOL.4: 2 residues within 4Å: Chain A: Y.343, E.345 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.345 GOL.5: 5 residues within 4Å: Chain A: K.293, C.294, S.296, E.345, R.463 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.293, A:E.345 Water bridges: A:E.345, A:R.463 GOL.6: 3 residues within 4Å: Chain A: R.498, V.499, G.500 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.497, A:R.498 GOL.7: 6 residues within 4Å: Chain A: R.215, F.216, F.221, G.222, W.225, R.348 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.215, A:R.215, A:R.215 Water bridges: A:R.348 GOL.8: 5 residues within 4Å: Chain A: W.54, R.57, K.432, D.435, E.438 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.57, A:D.435, A:E.438 GOL.9: 4 residues within 4Å: Chain A: L.305, Q.471, I.472, P.477 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.303 GOL.12: 2 residues within 4Å: Chain B: K.497, R.498 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.497 GOL.13: 3 residues within 4Å: Chain B: Y.343, E.345, G.351 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.345 Water bridges: B:D.350, B:D.350 GOL.14: 10 residues within 4Å: Chain B: Q.372, K.386, R.387, E.389, K.403, E.417, Q.502, Y.503, E.504 Ligands: NAP.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.387, B:K.403, B:K.403, B:E.504 GOL.15: 1 residues within 4Å: Chain B: R.227 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.227, B:R.227

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
L

B
C

Glucose-6-phosphate 1-dehydrogenase

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