SMTL ID : 9csl.1

Structure of mutant human geranylgeranyl pyrophosphate synthase (Y246D-C247L) in complex with isopentenyl pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

1 x IPE: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

IPE.1: 10 residues within 4Å: Chain A: G.46, K.47, V.49, R.50, H.79, L.83, R.96, T.174, Q.207, D.210 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.83 Hydrogen bonds: A:K.47 Water bridges: A:K.47, A:K.47, A:Q.48, A:Q.48, A:R.50, A:R.50, A:R.50, A:N.80, A:R.95 Salt bridges: A:K.47, A:K.47, A:R.50, A:H.79, A:H.79, A:R.96

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 1 residues within 4Å: Chain A: H.59 Ligand excluded by PLIP

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

SO4.3: 3 residues within 4Å: Chain A: S.92, K.93, L.94 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.93, A:L.94 Water bridges: A:S.92, A:L.94 Salt bridges: A:K.234 SO4.4: 2 residues within 4Å: Chain A: P.197, N.200 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.200 Water bridges: A:K.292, A:K.292, A:Q.296 SO4.5: 5 residues within 4Å: Chain A: G.277, S.278, F.279, E.280, R.283 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.278, A:F.279, A:E.280, A:R.283 Water bridges: A:R.283 SO4.6: 3 residues within 4Å: Chain A: E.280, R.283, K.287 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.280 Salt bridges: A:R.283, A:K.287 SO4.7: 2 residues within 4Å: Chain A: H.312, K.315 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.312, A:K.315 SO4.8: 3 residues within 4Å: Chain B: L.83, R.95, R.96 5 PLIP interactions: 5 interactions with chain B Water bridges: B:D.86, B:R.95, B:R.96 Salt bridges: B:R.95, B:R.96 SO4.9: 2 residues within 4Å: Chain B: A.299, R.300 7 PLIP interactions: 7 interactions with chain B Water bridges: B:A.299, B:R.300, B:R.300, B:R.300, B:R.300, B:R.300 Salt bridges: B:R.300 SO4.10: 2 residues within 4Å: Chain B: P.197, N.200 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.200 Water bridges: B:K.292, B:K.292, B:K.292, B:Q.296 Salt bridges: B:K.292 SO4.11: 2 residues within 4Å: Chain B: E.280, R.283 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.283, B:K.287 SO4.12: 6 residues within 4Å: Chain B: K.47, Q.48, V.49, R.50, H.79, R.96 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.47, B:Q.48, B:V.49, B:R.96 Water bridges: B:R.50, B:R.50 Salt bridges: B:R.50, B:H.79 SO4.13: 3 residues within 4Å: Chain B: K.47, R.209, Y.220 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.209 SO4.14: 2 residues within 4Å: Chain B: H.312, K.315 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.312, B:K.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ezekiel, S.J. et al., Engineering dimer mutants of human geranylgeranyl pyrophosphate synthase. Plos One (2025)

Release Date

2025-01-29

Peptides

Geranylgeranyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Geranylgeranyl pyrophosphate synthase