SMTL ID : 2bhl.1

X-RAY STRUCTURE OF HUMAN GLUCOSE-6-PHOSPHATE DEHYDROGENASE (DELETION VARIANT) COMPLEXED WITH GLUCOSE-6-PHOSPHATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: S.270, E.271, V.272, Q.273, N.276, V.315, Y.317, E.319 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.270, A:Q.273, A:N.276, A:V.315, A:Y.317 GOL.2: 5 residues within 4Å: Chain A: A.274, V.277, L.279, Q.445, P.451 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.274 GOL.3: 7 residues within 4Å: Chain A: E.321 Chain D: R.189, F.190, F.195, G.196, W.199, R.322 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:R.189, D:F.195, A:E.321 GOL.4: 7 residues within 4Å: Chain A: R.189, F.190, G.196, W.199, K.249, R.322 Chain D: E.321 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.189, A:R.189, A:R.322 Water bridges: A:K.249 GOL.6: 5 residues within 4Å: Chain B: W.28, R.31, K.63, K.406, E.412 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.31, B:R.31, B:K.63, B:K.406 GOL.7: 5 residues within 4Å: Chain B: G.137, W.138, N.139, R.166, Q.169 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.139, B:N.139, B:R.166, B:Q.169 GOL.9: 8 residues within 4Å: Chain C: S.270, E.271, V.272, Q.273, N.276, V.315, Y.317, E.319 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.270, C:Q.273, C:N.276, C:V.315, C:Y.317 GOL.10: 5 residues within 4Å: Chain C: A.274, V.277, L.279, Q.445, P.451 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.274 GOL.11: 7 residues within 4Å: Chain B: R.189, F.190, F.195, G.196, W.199, R.322 Chain C: E.321 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:E.321, B:R.189, B:F.195 GOL.12: 7 residues within 4Å: Chain B: E.321 Chain C: R.189, F.190, G.196, W.199, K.249, R.322 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.189, C:R.189, C:R.322 Water bridges: C:K.249 GOL.14: 5 residues within 4Å: Chain D: W.28, R.31, K.63, K.406, E.412 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.31, D:R.31, D:K.63, D:K.406 GOL.15: 5 residues within 4Å: Chain D: G.137, W.138, N.139, R.166, Q.169 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.139, D:N.139, D:R.166, D:Q.169

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

BG6.5: 10 residues within 4Å: Chain A: K.145, H.175, Y.176, K.179, E.213, D.232, H.237, K.334, R.339, Q.369 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.145, A:K.145, A:Y.176, A:D.232, A:K.334, A:K.334, A:Q.369 Water bridges: A:R.339, A:R.339 Salt bridges: A:K.145, A:H.175, A:H.175, A:K.179, A:H.237, A:R.339 BG6.8: 11 residues within 4Å: Chain B: K.145, H.175, Y.176, K.179, F.211, E.213, D.232, H.237, K.334, R.339, Q.369 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.145, B:K.145, B:D.232, B:K.334, B:K.334, B:Q.369 Salt bridges: B:K.145, B:H.175, B:H.175, B:K.179, B:H.237, B:R.339 BG6.13: 10 residues within 4Å: Chain C: K.145, H.175, Y.176, K.179, E.213, D.232, H.237, K.334, R.339, Q.369 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:K.145, C:K.145, C:D.232, C:K.334, C:K.334, C:Q.369 Water bridges: C:R.339, C:R.339 Salt bridges: C:K.145, C:H.175, C:H.175, C:K.179, C:H.237, C:R.339 BG6.16: 11 residues within 4Å: Chain D: K.145, H.175, Y.176, K.179, F.211, E.213, D.232, H.237, K.334, R.339, Q.369 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:K.145, D:K.145, D:Y.176, D:D.232, D:K.334, D:K.334, D:Q.369 Water bridges: D:H.175 Salt bridges: D:K.145, D:H.175, D:H.175, D:K.179, D:H.237, D:R.339

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kotaka, M. et al., Structural Studies of Glucose-6-Phosphate and Nadp+ Binding to Human Glucose-6-Phosphate Dehydrogenase. Acta Crystallogr.,Sect.D (2005)

Release Date

2005-04-25

Peptides

GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE

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