SMTL ID : 5fb3.1

Structure of glycerophosphate dehydrogenase in complex with NADPH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.108, D.157, H.238, H.256 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.157, A:H.238, A:H.256 ZN.5: 4 residues within 4Å: Chain B: D.108, D.157, H.238, H.256 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.157, B:H.238, B:H.256 ZN.9: 4 residues within 4Å: Chain C: D.108, D.157, H.238, H.256 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.157, C:H.238, C:H.256 ZN.13: 4 residues within 4Å: Chain D: D.108, D.157, H.238, H.256 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.157, D:H.238, D:H.256 ZN.16: 3 residues within 4Å: Chain E: D.157, H.238, H.256 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.157, E:H.238, E:H.256 ZN.20: 3 residues within 4Å: Chain F: D.157, H.238, H.256 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.157, F:H.238, F:H.256, H2O.6

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: S.116, F.117, S.230, S.234, H.242, R.312 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.117, A:S.230, A:S.230, A:S.234 Salt bridges: A:H.242, A:R.312 SO4.3: 4 residues within 4Å: Chain A: Y.92, Y.126, G.127, K.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.92, A:K.128 SO4.4: 6 residues within 4Å: Chain A: E.58, I.60, Q.64, V.65, E.66, K.69 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.66, A:E.66 Salt bridges: A:K.69 SO4.6: 5 residues within 4Å: Chain A: K.200 Chain B: R.173 Chain D: Y.269, W.275, R.276 7 PLIP interactions: 3 interactions with chain D, 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: D:R.276, D:R.276 Water bridges: D:W.275, B:R.173, B:R.173 Salt bridges: B:R.173, A:K.200 SO4.7: 4 residues within 4Å: Chain B: P.70, G.71, F.72, K.96 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.71, B:F.72 Salt bridges: B:K.96 SO4.10: 6 residues within 4Å: Chain C: S.116, F.117, S.230, S.234, H.242, R.312 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:F.117, C:S.230, C:S.234 Salt bridges: C:H.242, C:R.312 SO4.11: 5 residues within 4Å: Chain C: E.5, Y.179, S.180, E.181 Chain D: K.215 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Salt bridges: D:R.211, D:K.215 Hydrogen bonds: C:Y.179, C:E.181 SO4.14: 3 residues within 4Å: Chain D: S.290, R.292, Q.293 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.290, D:S.290, D:Q.293 Salt bridges: D:R.292 SO4.17: 6 residues within 4Å: Chain E: Y.114, G.228, S.229, S.230, R.312, R.315 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:S.230 Salt bridges: E:K.128, E:R.312, E:R.315 SO4.18: 3 residues within 4Å: Chain C: R.166, G.272 Chain F: R.166 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Salt bridges: F:R.166, C:R.166 SO4.21: 3 residues within 4Å: Chain F: S.40, S.41, K.44 3 PLIP interactions: 3 interactions with chain F Water bridges: F:S.41, F:K.44 Salt bridges: F:K.44 SO4.22: 5 residues within 4Å: Chain F: P.70, G.71, F.72, H.94, K.96 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.71, F:F.72 Salt bridges: F:H.94, F:K.96

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.8: 6 residues within 4Å: Chain B: G.80, G.81, R.82, S.104, S.106, L.150 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.81, B:S.104, B:S.106 Water bridges: B:Y.62 Salt bridges: B:R.82

3 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.12: 28 residues within 4Å: Chain D: G.38, K.39, S.40, S.41, T.42, Y.45, G.80, G.81, R.82, P.83, D.85, T.103, S.104, S.106, H.107, D.108, G.109, Y.114, V.115, S.116, L.119, I.142, S.145, A.146, P.147, L.150, E.251, H.256 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:H.256 Hydrogen bonds: D:K.39, D:S.40, D:S.40, D:S.40, D:S.41, D:S.41, D:T.42, D:G.81, D:R.82, D:R.82, D:D.85, D:D.85, D:T.103, D:S.104, D:S.106, D:S.116, D:E.251 Water bridges: D:G.80, D:G.80 pi-Stacking: D:H.256 NDP.15: 26 residues within 4Å: Chain E: G.38, K.39, S.40, S.41, T.42, G.80, G.81, R.82, P.83, D.85, T.103, S.104, S.106, H.107, G.109, Y.114, V.115, S.116, I.142, S.145, A.146, P.147, L.150, E.245, D.252, H.256 22 PLIP interactions: 22 interactions with chain E Hydrophobic interactions: E:H.256 Hydrogen bonds: E:K.39, E:S.40, E:S.40, E:S.41, E:S.41, E:T.42, E:T.42, E:Y.62, E:G.81, E:R.82, E:R.82, E:R.82, E:D.85, E:D.85, E:T.103, E:S.106, E:D.252 Water bridges: E:S.112, E:S.116 pi-Stacking: E:H.107, E:H.256 NDP.19: 26 residues within 4Å: Chain F: G.38, K.39, S.40, S.41, T.42, Y.45, G.80, G.81, R.82, P.83, D.85, T.103, S.104, S.106, H.107, G.109, Y.114, V.115, S.116, I.142, S.145, A.146, P.147, L.150, E.251, H.256 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:H.256 Hydrogen bonds: F:K.39, F:S.40, F:S.40, F:T.42, F:T.42, F:G.81, F:R.82, F:R.82, F:R.82, F:D.85, F:T.103, F:S.106 Water bridges: F:K.88, F:S.112, F:S.116, F:S.116 Salt bridges: F:R.82 pi-Stacking: F:H.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hayashi, J. et al., Unique coenzyme binding mode of hyperthermophilic archaeal sn-glycerol-1-phosphate dehydrogenase from Pyrobaculum calidifontis. Proteins (2016)

Release Date

2016-10-12

Peptides

Glycerol-1-phosphate dehydrogenase [NAD(P)+]: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Glycerol-1-phosphate dehydrogenase [NAD(P)+]