SMTL ID : 1x09.1

Crystal structure of the D26A mutant UPPs in complex with magnesium and isopentenyl pyrophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: R.194, R.200 Ligands: IPE.2, IPE.3 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: R.194, R.200 Ligands: IPE.5, IPE.6 No protein-ligand interaction detected (PLIP)

4 x IPE: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

IPE.2: 10 residues within 4Å: Chain A: M.25, A.26, G.27, N.28, G.29, R.30, R.39, H.43 Ligands: MG.1, IPE.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:M.25, A:G.27, A:N.28, A:N.28, A:G.29, A:R.30 Water bridges: A:R.30, A:R.77, A:R.77, A:R.77, A:R.194 Salt bridges: A:R.39, A:R.39, A:H.43 IPE.3: 14 residues within 4Å: Chain A: I.24, M.25, A.26, Y.68, A.69, F.70, N.74, R.77, R.194, R.200, S.202 Chain B: Y.211 Ligands: MG.1, IPE.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.24, A:A.26, A:Y.68, A:Y.68, A:Y.68 Hydrogen bonds: A:S.71, A:N.74, A:R.77, A:S.202, A:S.202 Water bridges: A:R.194, A:R.194, A:R.200, A:R.200, A:R.200, A:R.200 Salt bridges: A:R.194, A:R.194, A:R.200 IPE.5: 10 residues within 4Å: Chain B: M.25, A.26, G.27, N.28, G.29, R.30, R.39, H.43 Ligands: MG.4, IPE.6 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:M.25, B:G.27, B:N.28, B:N.28, B:G.29, B:R.30 Water bridges: B:R.30, B:R.77, B:R.77, B:R.77, B:R.194 Salt bridges: B:R.39, B:R.39, B:H.43 IPE.6: 14 residues within 4Å: Chain A: Y.211 Chain B: I.24, M.25, A.26, Y.68, A.69, F.70, N.74, R.77, R.194, R.200, S.202 Ligands: MG.4, IPE.5 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.24, B:A.26, B:Y.68, B:Y.68, B:Y.68 Hydrogen bonds: B:S.71, B:N.74, B:R.77, B:S.202, B:S.202 Water bridges: B:R.194, B:R.194, B:R.200, B:R.200, B:R.200, B:R.200, A:Y.211 Salt bridges: B:R.194, B:R.194, B:R.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, R.T. et al., Crystal structures of undecaprenyl pyrophosphate synthase in complex with magnesium, isopentenyl pyrophosphate, and farnesyl thiopyrophosphate: roles of the metal ion and conserved residues in catalysis. J.Biol.Chem. (2005)

Release Date

2005-03-22

Peptides

Undecaprenyl pyrophosphate synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Undecaprenyl pyrophosphate synthetase

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