SMTL ID : 3vzy.1

Crystal structure of PcrB complexed with G1P from bacillus subtilis subap. subtilis str. 168

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: R.56, F.58 Ligands: MG.6 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:R.56, A:F.58, H2O.2, H2O.2, H2O.2, H2O.7 MG.2: 2 residues within 4Å: Chain A: D.203 Ligands: MG.5 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.203, H2O.1, H2O.1, H2O.7, H2O.9, H2O.12 MG.3: 2 residues within 4Å: Chain A: G.39, S.40 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.3, H2O.7, H2O.7, H2O.10, H2O.11 MG.4: 2 residues within 4Å: Chain A: R.56, G.75 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: T.5 Ligands: MG.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:T.5, H2O.1, H2O.1, H2O.1, H2O.7, H2O.9 MG.6: 2 residues within 4Å: Chain A: D.77 Ligands: MG.1 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain B: R.56, F.58 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:R.56, B:F.58, H2O.15, H2O.15, H2O.16, H2O.16 MG.13: 2 residues within 4Å: Chain B: T.5 Ligands: MG.14 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.5, H2O.13, H2O.13, H2O.14, H2O.16 MG.14: 2 residues within 4Å: Chain B: D.203 Ligands: MG.13 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.203, H2O.13, H2O.16, H2O.16, H2O.18 MG.15: 2 residues within 4Å: Chain B: E.45, D.46 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.45, B:D.46

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 2 residues within 4Å: Chain A: F.58, L.59 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: Y.2, W.7 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: S.162, G.188 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: D.18, L.19, L.24, M.51, K.54 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: T.44, E.45 Ligand excluded by PLIP

1 x 1GP: SN-GLYCEROL-1-PHOSPHATE(Non-covalent)

1GP.11: 11 residues within 4Å: Chain B: K.12, Y.158, E.160, S.162, G.163, G.186, G.187, G.188, V.206, G.208, N.209 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:E.160, B:S.162, B:G.188, B:G.208, B:N.209, B:N.209 Water bridges: B:E.160, B:G.187, B:I.189, B:A.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, F. et al., Insights into TIM-barrel prenyl transferase mechanisms: crystal structures of PcrB from Bacillus subtilis and Staphylococcus aureus. Chembiochem (2013)

Release Date

2012-12-26

Peptides

Heptaprenylglyceryl phosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heptaprenylglyceryl phosphate synthase

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