SMTL ID : 1qki.1 (1 other biounit)

X-RAY STRUCTURE OF HUMAN GLUCOSE 6-PHOSPHATE DEHYDROGENASE (VARIANT CANTON R459L) COMPLEXED WITH STRUCTURAL NADP+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 18 residues within 4Å: Chain A: K.237, R.356, E.363, K.365, R.369, R.392, A.398, Y.400, K.402, D.420, T.422, R.486, D.492, M.495, F.500, Y.502, Y.506, W.508 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.400, A:Y.400, A:W.508 Hydrogen bonds: A:E.363, A:E.367, A:E.367, A:R.392, A:T.422, A:R.486, A:R.486, A:Y.502 Salt bridges: A:K.237, A:R.356, A:K.365, A:R.369, A:R.369, A:K.402, A:K.402, A:R.486 pi-Stacking: A:Y.502, A:Y.502 pi-Cation interactions: A:R.486 NAP.3: 18 residues within 4Å: Chain B: K.237, R.356, E.363, K.365, R.369, R.392, A.398, Y.400, K.402, D.420, T.422, R.486, D.492, M.495, F.500, Y.502, Y.506, W.508 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Y.400, B:Y.400 Hydrogen bonds: B:R.392, B:Y.400, B:T.422, B:R.486 Salt bridges: B:K.237, B:R.356, B:K.365, B:R.369, B:R.369, B:K.402, B:K.402, B:R.486 pi-Stacking: B:Y.502, B:Y.502, B:W.508, B:W.508 pi-Cation interactions: B:R.486 NAP.7: 18 residues within 4Å: Chain C: K.237, R.356, E.363, K.365, R.369, R.392, A.398, Y.400, K.402, D.420, T.422, R.486, D.492, M.495, F.500, Y.502, Y.506, W.508 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:E.363, C:R.369, C:R.392, C:T.422, C:R.486, C:R.486, C:D.492 Salt bridges: C:K.237, C:R.356, C:K.365, C:R.369, C:R.369, C:K.402, C:K.402, C:R.486 pi-Stacking: C:Y.400, C:Y.502, C:Y.502, C:W.508, C:W.508 pi-Cation interactions: C:R.486, C:R.486 NAP.10: 17 residues within 4Å: Chain D: K.237, R.356, E.363, K.365, R.369, R.392, Y.400, K.402, D.420, T.422, R.486, D.492, M.495, F.500, Y.502, Y.506, W.508 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:R.392, D:Y.400, D:T.422, D:R.486 Salt bridges: D:K.237, D:R.356, D:K.365, D:R.369, D:R.369, D:K.402, D:K.402, D:R.486 pi-Stacking: D:Y.400, D:Y.502, D:Y.502, D:W.508, D:W.508 pi-Cation interactions: D:R.486, D:R.486

4 x GOA: GLYCOLIC ACID(Non-covalent)

GOA.2: 3 residues within 4Å: Chain A: K.46, H.200, K.204 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.204 Salt bridges: A:K.46, A:H.200, A:K.204 GOA.4: 4 residues within 4Å: Chain B: K.46, H.200, Y.201, K.204 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.201, B:R.364 Salt bridges: B:K.46, B:H.200, B:K.204 GOA.8: 4 residues within 4Å: Chain C: H.200, Y.201, K.204, R.364 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.201 Salt bridges: C:K.46, C:K.204, C:R.364 GOA.11: 4 residues within 4Å: Chain D: K.46, H.200, Y.201, K.204 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.46, D:Y.201 Salt bridges: D:H.200, D:K.204, D:R.364

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: R.218 Chain B: H.373, D.374 Chain D: R.226, D.349 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.218, A:R.218, D:R.226 GOL.6: 4 residues within 4Å: Chain B: R.226, D.349 Chain D: H.373, D.374 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:D.374, B:R.226 GOL.9: 3 residues within 4Å: Chain A: H.373, D.374 Chain C: R.226 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.374, C:R.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Au, S.W.N. et al., Human Glucose-6-Phosphate Dehydrogenase: The Crystal Structure Reveals a Structural Nadp+ Molecule and Provides Insights Into Enzyme Deficiency. Structure (2000)

Release Date

2000-03-16

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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