SMTL ID : 2q80.1

Crystal structure of human geranylgeranyl pyrophosphate synthase bound to GGPP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.65, D.69, Q.127 Ligands: MG.2, GRG.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.65, A:D.69 MG.2: 6 residues within 4Å: Chain A: D.65, D.69, K.203, E.211 Ligands: MG.1, GRG.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.65, A:D.69 MG.4: 6 residues within 4Å: Chain B: D.65, D.69, Q.127, D.130 Ligands: MG.5, GRG.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.65, B:D.69 MG.5: 5 residues within 4Å: Chain B: D.65, D.69, E.211 Ligands: MG.4, GRG.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.65, B:D.69 MG.7: 6 residues within 4Å: Chain C: D.65, D.69, Q.127, D.130 Ligands: MG.8, GRG.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.65, C:D.69 MG.8: 6 residues within 4Å: Chain C: D.65, D.66, D.69, E.211 Ligands: MG.7, GRG.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.65, C:D.69 MG.10: 6 residues within 4Å: Chain D: D.65, D.69, Q.127, D.130 Ligands: MG.11, GRG.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.65, D:D.69 MG.11: 6 residues within 4Å: Chain D: D.65, D.69, S.71, E.211 Ligands: MG.10, GRG.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.65, D:D.69 MG.13: 6 residues within 4Å: Chain E: D.65, D.69, D.130, E.211 Ligands: MG.14, GRG.15 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.65, E:D.69 MG.14: 5 residues within 4Å: Chain E: D.65, D.69, E.211 Ligands: MG.13, GRG.15 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.65, E:D.69 MG.16: 6 residues within 4Å: Chain F: D.65, D.69, Q.127, D.130 Ligands: MG.17, GRG.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.65, F:D.69 MG.17: 5 residues within 4Å: Chain F: D.65, D.69, K.203 Ligands: MG.16, GRG.18 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.65, F:D.65, F:D.69

6 x GRG: GERANYLGERANYL DIPHOSPHATE(Non-covalent)

GRG.3: 20 residues within 4Å: Chain A: L.32, S.33, T.54, H.58, D.65, D.69, R.74, Q.127, K.152, T.153, L.156, F.157, A.160, V.161, Q.186, D.189, K.203, K.213 Ligands: MG.1, MG.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.32, A:L.32, A:T.54, A:K.152, A:T.153, A:L.156, A:F.157, A:A.160, A:V.161 Hydrogen bonds: A:D.65, A:D.69, A:Q.186 Salt bridges: A:R.74, A:K.152, A:K.203, A:K.203, A:K.213 GRG.6: 20 residues within 4Å: Chain B: R.29, L.32, S.33, T.54, H.58, S.61, D.65, D.69, R.74, Q.127, K.152, L.156, F.157, A.160, Q.186, D.189, K.203, K.213 Ligands: MG.4, MG.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.32, B:H.58, B:F.157, B:F.157, B:A.160 Hydrogen bonds: B:Q.186, B:D.189 Salt bridges: B:R.74, B:K.152, B:K.203, B:K.213 GRG.9: 23 residues within 4Å: Chain C: R.29, L.32, S.33, F.36, T.54, H.58, D.65, D.69, R.74, L.123, Q.127, D.130, K.152, T.153, L.156, F.157, A.160, M.164, Q.186, D.189, K.213 Ligands: MG.7, MG.8 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:R.29, C:L.32, C:L.32, C:F.36, C:H.58, C:L.123, C:T.153, C:F.157, C:A.160 Hydrogen bonds: C:Q.186, C:D.189 Salt bridges: C:R.74, C:K.152, C:K.213 GRG.12: 21 residues within 4Å: Chain D: R.29, S.33, T.54, H.58, D.65, D.69, R.74, L.123, Q.127, K.152, T.153, L.156, F.157, A.160, V.161, Q.186, D.189, K.203, K.213 Ligands: MG.10, MG.11 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:R.29, D:T.54, D:H.58, D:L.123, D:K.152, D:T.153, D:L.156, D:F.157, D:F.157, D:A.160, D:V.161 Hydrogen bonds: D:Q.186 Salt bridges: D:R.74, D:K.152, D:K.203, D:K.213 GRG.15: 21 residues within 4Å: Chain E: L.32, S.33, F.36, T.54, H.58, D.65, D.69, R.74, D.130, K.152, T.153, L.156, F.157, A.160, V.161, Q.186, D.189, K.203, K.213 Ligands: MG.13, MG.14 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:L.32, E:F.36, E:H.58, E:K.152, E:T.153, E:F.157, E:F.157, E:A.160, E:V.161 Hydrogen bonds: E:D.65, E:Q.186 Salt bridges: E:R.74, E:K.152, E:K.203, E:K.213 GRG.18: 13 residues within 4Å: Chain F: D.65, D.69, R.74, Q.127, K.152, T.153, L.156, F.157, Q.186, D.189, K.203 Ligands: MG.16, MG.17 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:T.153, F:F.157 Hydrogen bonds: F:D.65, F:Q.186, F:D.189 Salt bridges: F:R.74, F:K.152, F:K.203, F:K.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kavanagh, K.L. et al., The crystal structure of human geranylgeranyl pyrophosphate synthase reveals a novel hexameric arrangement and inhibitory product binding. J.Biol.Chem. (2006)

Release Date

2007-06-19

Peptides

Geranylgeranyl pyrophosphate synthetase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Geranylgeranyl pyrophosphate synthetase