SMTL ID : 6nke.1

Wild-type GGGPS from Thermoplasma volcanium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: L.20, F.77, Y.170, E.172, S.175, G.200, G.201, V.221 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.200 Water bridges: A:G.223 GOL.2: 10 residues within 4Å: Chain A: P.78, S.81, N.82, I.84, I.91, F.92, F.93, M.94, H.108, Q.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.82, A:F.92, A:M.94, A:H.108 GOL.6: 9 residues within 4Å: Chain B: L.20, F.77, Y.170, E.172, S.175, G.200, G.201, V.221 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.170, B:G.200 Water bridges: B:G.223 GOL.7: 10 residues within 4Å: Chain B: P.78, S.81, N.82, I.84, I.91, F.92, F.93, M.94, H.108, Q.109 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.82, B:F.92, B:M.94, B:H.108

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

SO4.3: 8 residues within 4Å: Chain A: G.174, S.175, G.176, A.177, G.201, G.202, R.204 Ligands: GOL.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.174, A:G.176, A:A.177, A:G.201, A:G.202 Water bridges: A:I.203, A:G.223, A:G.223, A:G.223, A:G.223 Salt bridges: A:R.204 SO4.8: 8 residues within 4Å: Chain B: G.174, S.175, G.176, A.177, G.201, G.202, R.204 Ligands: GOL.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.174, B:G.176, B:A.177, B:G.201, B:G.202 Water bridges: B:I.203, B:G.223, B:G.223, B:G.223, B:G.223 Salt bridges: B:R.204

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 2 residues within 4Å: Chain A: Q.6, K.73 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.73 Water bridges: A:Q.6, A:K.73 pi-Cation interactions: A:K.73 IMD.5: 4 residues within 4Å: Chain A: Q.162, Y.163, N.194 Chain B: K.123 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.123 Water bridges: B:I.121, A:Q.162 IMD.9: 2 residues within 4Å: Chain B: Q.6, K.73 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.73 Water bridges: B:Q.6, B:K.73 pi-Cation interactions: B:K.73 IMD.10: 4 residues within 4Å: Chain A: K.123 Chain B: Q.162, Y.163, N.194 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.163, A:K.123 Water bridges: B:Q.162, A:I.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blank, P.N. et al., Structural studies of geranylgeranylglyceryl phosphate synthase, a prenyltransferase found in thermophilic Euryarchaeota. Acta Crystallogr D Struct Biol (2020)

Release Date

2019-01-23

Peptides

Geranylgeranylglyceryl phosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Geranylgeranylglyceryl phosphate synthase