SMTL ID : 6g31.1 (1 other biounit)

Crystal structure of human geranylgeranyl diphosphate synthase mutant D188Y bound to zoledronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-hexamer

Ligands

6 x ZOL: ZOLEDRONIC ACID(Non-covalent)

ZOL.1: 10 residues within 4Å: Chain A: D.71, D.75, R.80, Q.133, K.158, Q.192, K.219 Ligands: MG.2, MG.3, MG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.80, A:R.80, A:K.158, A:Q.192, A:Q.192, A:Q.192, A:K.219 ZOL.5: 9 residues within 4Å: Chain B: D.71, D.75, R.80, Q.133, K.158, Q.192 Ligands: MG.6, MG.7, MG.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.80, B:R.80, B:Q.192, B:Q.192 ZOL.9: 7 residues within 4Å: Chain C: L.68, D.71, D.75, R.80 Ligands: MG.10, MG.11, MG.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.80, C:R.80 ZOL.13: 8 residues within 4Å: Chain D: D.71, D.75, R.80, Q.133, Q.192 Ligands: MG.14, MG.15, MG.16 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.80, D:Q.192 ZOL.17: 7 residues within 4Å: Chain E: D.71, D.75, K.158, Q.192 Ligands: MG.18, MG.19, MG.20 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.192 ZOL.21: 9 residues within 4Å: Chain F: L.68, D.71, D.75, R.80, Q.133, Q.192 Ligands: MG.22, MG.23, MG.24 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.80, F:Q.192

18 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 4 residues within 4Å: Chain A: Q.192, D.196, K.219 Ligands: ZOL.1 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain A: D.71, D.72, D.75 Ligands: ZOL.1, MG.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.71, A:D.75 MG.4: 6 residues within 4Å: Chain A: D.71, D.75, Q.133, D.136 Ligands: ZOL.1, MG.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.71, A:D.75 MG.6: 3 residues within 4Å: Chain B: D.196, D.214 Ligands: ZOL.5 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain B: D.71, D.75, R.80 Ligands: ZOL.5, MG.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.71, B:D.75 MG.8: 5 residues within 4Å: Chain B: D.71, D.75, Q.133 Ligands: ZOL.5, MG.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.71, B:D.75, B:D.75 MG.10: 2 residues within 4Å: Chain C: Y.195 Ligands: ZOL.9 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain C: D.71, D.75 Ligands: ZOL.9, MG.12 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.71, C:D.75 MG.12: 4 residues within 4Å: Chain C: D.71, D.75 Ligands: ZOL.9, MG.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.71, C:D.75, C:D.75 MG.14: 2 residues within 4Å: Chain D: D.196 Ligands: ZOL.13 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain D: D.71, D.75 Ligands: ZOL.13 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.71, D:D.75 MG.16: 4 residues within 4Å: Chain D: D.71, D.75, D.136 Ligands: ZOL.13 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.75, D:D.75 MG.18: 3 residues within 4Å: Chain E: Y.195, D.196 Ligands: ZOL.17 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain E: D.71, D.75 Ligands: ZOL.17 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.71, E:D.75 MG.20: 3 residues within 4Å: Chain E: D.71, D.75 Ligands: ZOL.17 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.71, E:D.75 MG.22: 1 residues within 4Å: Ligands: ZOL.21 No protein-ligand interaction detected (PLIP) MG.23: 6 residues within 4Å: Chain F: D.71, D.75, S.77, E.217 Ligands: ZOL.21, MG.24 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.71, F:D.75 MG.24: 6 residues within 4Å: Chain F: D.71, D.75, Q.133, D.136 Ligands: ZOL.21, MG.23 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.71, F:D.75, F:D.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lisnyansky, M. et al., Reduced Activity of Geranylgeranyl Diphosphate Synthase Mutant Is Involved in Bisphosphonate-Induced Atypical Fractures. Mol. Pharmacol. (2018)

Release Date

2018-10-17

Peptides

Geranylgeranyl pyrophosphate synthase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

E
I

F
J

Geranylgeranyl pyrophosphate synthase

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