SMTL ID : 1t0a.1

Crystal Structure of 2C-Methyl-D-Erythritol-2,4-cyclodiphosphate Synthase from Shewanella Oneidensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.10, H.12, H.44 Ligands: CO.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.10, A:H.12, A:H.44, H2O.2, H2O.8 ZN.4: 4 residues within 4Å: Chain B: D.10, H.12, H.44 Ligands: CO.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.10, B:H.12, B:H.44, H2O.15 ZN.6: 4 residues within 4Å: Chain C: D.10, H.12, H.44 Ligands: CO.7 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.10, C:H.12, C:H.44, H2O.15

3 x CO: COBALT (II) ION(Non-covalent)

CO.2: 3 residues within 4Å: Chain A: D.10 Chain B: T.134 Ligands: ZN.1 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:T.134, A:D.10, H2O.1, H2O.8, H2O.10 CO.5: 3 residues within 4Å: Chain B: D.10 Chain C: T.134 Ligands: ZN.4 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: B:D.10, C:T.134, H2O.8, H2O.16, H2O.17 CO.7: 3 residues within 4Å: Chain A: T.134 Chain C: D.10 Ligands: ZN.6 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:D.10, A:T.134, H2O.1, H2O.2, H2O.15

1 x FPP: FARNESYL DIPHOSPHATE(Non-covalent)

FPP.3: 17 residues within 4Å: Chain A: F.9, I.101, T.136, G.140, F.141, T.142, R.144, A.149 Chain B: F.9, G.140, F.141, R.144 Chain C: F.9, I.101, G.140, F.141, R.144 24 PLIP interactions: 7 interactions with chain B, 10 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: B:F.9, B:F.9, B:F.141, A:F.9, A:I.101, A:I.101, A:T.136, A:F.141, A:A.149, C:F.9, C:I.101, C:F.141 Hydrogen bonds: B:F.141, A:G.140, A:F.141, C:F.141 Water bridges: B:R.144, B:R.144, A:T.142, C:T.142, C:R.144 Salt bridges: B:R.144, A:R.144, C:R.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ni, S. et al., Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase from Shewanella oneidensis at 1.6 A: identification of farnesyl pyrophosphate trapped in a hydrophobic cavity. Acta Crystallogr.,Sect.D (2004)

Release Date

2004-10-26

Peptides

2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase