SMTL ID : 9hjs.1

Crystal structure of human geranylgeranyl diphosphate synthase mutant R235C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-hexamer

Ligands

6 x GRG: GERANYLGERANYL DIPHOSPHATE(Non-covalent)

GRG.1: 24 residues within 4Å: Chain A: S.39, F.42, T.60, H.64, S.67, L.68, D.71, D.75, R.80, Q.133, D.136, K.158, T.159, L.162, F.163, A.166, V.167, Q.192, D.195, N.199, K.209, K.219 Ligands: MG.2, MG.3 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:F.42, A:L.68, A:D.71, A:K.158, A:T.159, A:L.162, A:F.163, A:F.163, A:A.166, A:V.167 Hydrogen bonds: A:D.71, A:Q.192, A:D.195, A:N.199 Water bridges: A:S.77, A:R.80, A:Q.133, A:K.219, A:K.219 Salt bridges: A:R.80, A:K.158, A:K.209, A:K.219, A:K.219 GRG.4: 22 residues within 4Å: Chain B: L.38, S.39, F.42, T.60, H.64, D.71, D.75, R.80, L.129, Q.133, D.136, K.158, T.159, L.162, F.163, A.166, M.170, Q.192, D.195, N.199 Ligands: MG.5, MG.6 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.38, B:F.42, B:H.64, B:L.129, B:Q.133, B:K.158, B:L.162, B:L.162, B:F.163, B:F.163, B:A.166 Hydrogen bonds: B:D.71, B:Q.192, B:N.199 Salt bridges: B:R.80, B:K.158 GRG.7: 22 residues within 4Å: Chain C: R.35, L.38, S.39, T.60, H.64, D.71, D.75, R.80, L.129, Q.133, K.158, T.159, L.162, F.163, A.166, Q.192, D.195, N.199, K.209, K.219 Ligands: MG.8, MG.9 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:L.38, C:H.64, C:L.129, C:Q.133, C:K.158, C:L.162, C:L.162, C:F.163, C:F.163, C:A.166 Hydrogen bonds: C:D.71, C:Q.192, C:D.195 Water bridges: C:R.80, C:R.80 Salt bridges: C:R.80, C:K.158, C:K.209, C:K.219 GRG.10: 23 residues within 4Å: Chain D: S.39, F.42, T.60, H.64, L.68, D.71, D.75, R.80, L.129, Q.133, K.158, T.159, L.162, F.163, A.166, V.167, M.170, Q.192, D.195, K.209, K.219 Ligands: MG.11, MG.12 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:F.42, D:T.60, D:H.64, D:L.129, D:K.158, D:T.159, D:F.163, D:F.163, D:A.166, D:V.167 Hydrogen bonds: D:D.71, D:Q.192 Water bridges: D:R.80, D:Q.133, D:D.136 Salt bridges: D:R.80, D:K.158, D:K.209, D:K.219, D:K.219 GRG.13: 22 residues within 4Å: Chain E: L.38, S.39, F.42, T.60, H.64, S.67, L.68, D.71, D.75, R.80, Q.133, D.136, K.158, L.162, F.163, A.166, Q.192, D.195, K.209, K.219 Ligands: MG.14, MG.15 20 PLIP interactions: 20 interactions with chain E Hydrophobic interactions: E:L.38, E:L.38, E:F.42, E:T.60, E:L.68, E:Q.133, E:K.158, E:F.163, E:F.163, E:A.166 Hydrogen bonds: E:D.71, E:D.71, E:D.71, E:Q.192, E:N.199 Salt bridges: E:R.80, E:K.158, E:K.209, E:K.219, E:K.219 GRG.16: 20 residues within 4Å: Chain F: L.38, S.39, F.42, T.60, H.64, L.68, D.71, D.75, R.80, K.158, L.162, F.163, A.166, V.167, Q.192, D.195, K.209, K.219 Ligands: MG.17, MG.18 22 PLIP interactions: 22 interactions with chain F Hydrophobic interactions: F:L.38, F:L.38, F:F.42, F:H.64, F:L.68, F:D.71, F:K.158, F:F.163, F:F.163, F:F.163, F:A.166, F:V.167 Hydrogen bonds: F:Q.192, F:N.199 Water bridges: F:S.77, F:Q.133, F:K.209, F:K.219 Salt bridges: F:R.80, F:K.158, F:K.209, F:K.219

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.71, D.75, E.217 Ligands: GRG.1, MG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.71, A:D.75, H2O.1, H2O.1 MG.3: 5 residues within 4Å: Chain A: D.71, D.75, Q.133 Ligands: GRG.1, MG.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.71, A:D.75, A:D.75, H2O.1, H2O.1 MG.5: 4 residues within 4Å: Chain B: D.71, D.75, S.77 Ligands: GRG.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.71, B:D.75, H2O.1 MG.6: 5 residues within 4Å: Chain B: D.71, D.75, Q.133, D.136 Ligands: GRG.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.71, B:D.75, B:D.75, H2O.1 MG.8: 6 residues within 4Å: Chain C: D.71, D.75, Q.133, D.136 Ligands: GRG.7, MG.9 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.71, C:D.75, C:D.75, H2O.1, H2O.1 MG.9: 4 residues within 4Å: Chain C: D.71, D.75 Ligands: GRG.7, MG.8 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.71, C:D.75, H2O.2, H2O.2 MG.11: 5 residues within 4Å: Chain D: D.71, D.75, Q.133 Ligands: GRG.10, MG.12 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.71, D:D.71, H2O.2, H2O.2, H2O.2 MG.12: 5 residues within 4Å: Chain D: D.71, D.75, E.217 Ligands: GRG.10, MG.11 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.71, D:D.75, H2O.2 MG.14: 4 residues within 4Å: Chain E: D.71, D.75, S.77 Ligands: GRG.13 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.71, E:D.75 MG.15: 5 residues within 4Å: Chain E: D.71, D.75, Q.133, D.136 Ligands: GRG.13 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.71, E:D.75, H2O.3, H2O.3 MG.17: 6 residues within 4Å: Chain F: D.71, D.75, Q.133, D.136 Ligands: GRG.16, MG.18 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.71, F:D.75, H2O.3, H2O.3 MG.18: 7 residues within 4Å: Chain F: D.71, D.75, S.77, K.209, E.217 Ligands: GRG.16, MG.17 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.71, F:D.75, H2O.3

Links

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Citation

Yehia, R. et al., Crystal structure of human geranylgeranyl diphosphate synthase mutant R235C. To Be Published

Release Date

2025-06-25

Peptides

Geranylgeranyl pyrophosphate synthase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Geranylgeranyl pyrophosphate synthase