SMTL ID : 6r4v.1

Crystal structure of human geranylgeranyl diphosphate synthase bound to ibandronate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

17 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.71, D.75, R.80, K.209 Ligands: MG.3, BFQ.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.71, A:D.75, H2O.1, H2O.2 MG.2: 4 residues within 4Å: Chain A: Q.192, D.195, N.199 Ligands: BFQ.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.195, H2O.1, H2O.5 MG.3: 5 residues within 4Å: Chain A: D.71, D.75, Q.133 Ligands: MG.1, BFQ.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.71, A:D.75, H2O.1, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain B: D.71, D.75 Ligands: MG.7, BFQ.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.71, B:D.71, B:D.75, H2O.10, H2O.12 MG.7: 6 residues within 4Å: Chain B: D.71, D.75, Q.133, D.136 Ligands: MG.6, BFQ.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.71, B:D.75, H2O.9, H2O.10, H2O.11 MG.10: 4 residues within 4Å: Chain C: D.71, D.75 Ligands: MG.12, BFQ.13 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.71, C:D.75, H2O.18, H2O.18 MG.11: 4 residues within 4Å: Chain C: K.209, D.214, K.219 Ligands: BFQ.13 No protein-ligand interaction detected (PLIP) MG.12: 6 residues within 4Å: Chain C: D.71, D.75, Q.133, D.136 Ligands: MG.10, BFQ.13 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.71, C:D.75, H2O.19, H2O.19, H2O.20 MG.14: 5 residues within 4Å: Chain D: D.71, D.75, K.209 Ligands: MG.16, BFQ.17 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.71, D:D.75, H2O.25, H2O.27 MG.15: 3 residues within 4Å: Chain D: D.195, K.209 Ligands: BFQ.17 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.195, H2O.25, H2O.25, H2O.29 MG.16: 6 residues within 4Å: Chain D: D.71, D.75, Q.133, D.136 Ligands: MG.14, BFQ.17 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.71, D:D.75, H2O.25, H2O.27, H2O.27 MG.18: 4 residues within 4Å: Chain E: D.71, D.75 Ligands: MG.20, BFQ.21 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.71, E:D.75, H2O.34, H2O.35 MG.19: 3 residues within 4Å: Chain E: D.195, K.219 Ligands: BFQ.21 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.195, E:D.195, H2O.34, H2O.34 MG.20: 6 residues within 4Å: Chain E: D.71, D.75, Q.133, D.136 Ligands: MG.18, BFQ.21 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.71, E:D.75, H2O.33, H2O.34, H2O.35 MG.22: 4 residues within 4Å: Chain F: D.71, D.75 Ligands: MG.24, BFQ.25 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.71, F:D.75, H2O.43, H2O.43 MG.23: 3 residues within 4Å: Chain F: Q.192, D.195 Ligands: BFQ.25 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.195, H2O.42, H2O.42 MG.24: 6 residues within 4Å: Chain F: D.71, D.75, Q.133, D.136 Ligands: MG.22, BFQ.25 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.71, F:D.75, H2O.41, H2O.42, H2O.43

6 x BFQ: IBANDRONATE(Non-covalent)(Covalent)

BFQ.4: 15 residues within 4Å: Chain A: S.67, L.68, D.71, D.75, R.80, Y.103, Q.133, K.158, Q.192, D.195, K.209, K.219 Ligands: MG.1, MG.2, MG.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Q.133 Hydrogen bonds: A:R.80, A:R.80, A:K.158, A:Q.192, A:D.195, A:K.209, A:K.209, A:K.209, A:K.219 Water bridges: A:Q.133, A:D.136, A:K.158, A:N.199, A:N.199 Salt bridges: A:D.71 BFQ.8: 15 residues within 4Å: Chain B: S.67, L.68, I.70, D.71, D.75, R.80, Y.103, Q.133, K.158, Q.192, D.195, K.209, K.219 Ligands: MG.6, MG.7 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.70, B:Q.133 Hydrogen bonds: B:R.80, B:R.80, B:K.158, B:Q.192, B:Q.192, B:N.199, B:K.209, B:K.209, B:K.219 Water bridges: B:D.75, B:D.75, B:D.75, B:Q.133, B:D.136 Salt bridges: B:D.71 BFQ.13: 14 residues within 4Å: Chain C: S.67, L.68, D.71, D.75, R.80, L.129, Q.133, K.158, Q.192, K.209, K.219 Ligands: MG.10, MG.11, MG.12 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:D.71, C:L.129 Hydrogen bonds: C:D.71, C:R.80, C:R.80, C:Q.192, C:K.209, C:K.209, C:K.219 Water bridges: C:Q.133, C:K.158, C:K.158 Salt bridges: C:D.71 BFQ.17: 14 residues within 4Å: Chain D: S.67, D.71, D.75, R.80, Q.133, K.158, T.159, Q.192, D.195, K.209, K.219 Ligands: MG.14, MG.15, MG.16 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:R.80, D:R.80, D:Q.192, D:Q.192, D:D.195, D:D.195, D:K.209, D:K.209, D:K.219 Water bridges: D:D.136, D:K.158, D:N.199, D:K.209, D:E.217 Salt bridges: D:D.71 BFQ.21: 13 residues within 4Å: Chain E: S.67, D.71, D.75, R.80, L.129, Q.133, K.158, Q.192, D.195, K.219 Ligands: MG.18, MG.19, MG.20 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:D.71, E:Q.133 Hydrogen bonds: E:R.80, E:R.80, E:Q.192, E:K.219 Water bridges: E:D.71, E:S.77, E:Q.133 Salt bridges: E:D.71 BFQ.25: 16 residues within 4Å: Chain F: S.67, L.68, I.70, D.71, D.75, R.80, Y.103, L.129, Q.133, K.158, Q.192, D.195, K.219 Ligands: MG.22, MG.23, MG.24 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:I.70, F:D.71, F:Q.133 Hydrogen bonds: F:R.80, F:R.80, F:Q.192, F:K.219 Water bridges: F:D.71, F:D.75, F:S.77, F:S.77, F:S.77, F:Q.133 Salt bridges: F:D.71

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: G.31, K.32, R.35, H.64, F.191 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.32, A:K.32, A:K.32, A:R.35, A:R.35 GOL.9: 6 residues within 4Å: Chain B: G.31, K.32, R.35, H.64, R.81, F.191 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.32, B:R.35, B:R.35, B:H.64, B:R.81, B:R.81 Water bridges: B:R.80, B:D.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lisnyansky, M. et al., Metal Coordination Is Crucial for Geranylgeranyl Diphosphate Synthase-Bisphosphonate Interactions: A Crystallographic and Computational Analysis. Mol.Pharmacol. (2019)

Release Date

2019-09-18

Peptides

Geranylgeranyl pyrophosphate synthase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
F

D
E

E
B

F
D

Geranylgeranyl pyrophosphate synthase