SMTL ID : 3f0g.2 (1 other biounit)

Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase with CMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-trimer

Ligands

3 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.1: 11 residues within 4Å: Chain A: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156, E.158 Chain C: D.79, G.81 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:T.156 Hydrogen bonds: A:P.126, A:K.127, A:L.128, A:A.129, A:T.156, A:E.158, C:D.79, C:G.81 Water bridges: A:K.155, A:K.155, A:K.155, C:D.31 Salt bridges: A:K.155 pi-Cation interactions: A:K.127 C5P.3: 13 residues within 4Å: Chain A: D.79, G.81, R.82, D.86 Chain B: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156, E.158 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.156 Hydrogen bonds: B:A.123, B:L.128, B:A.129, B:T.156, B:E.158, B:E.158, B:E.158, A:D.79, A:G.81, A:R.82 Water bridges: B:A.154, B:K.155, B:K.155, B:K.155 Salt bridges: B:K.155 C5P.5: 10 residues within 4Å: Chain B: D.79, G.81 Chain C: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:D.79, B:G.81, C:A.123, C:L.128, C:A.129, C:T.156 Water bridges: B:D.31, C:K.155 Hydrophobic interactions: C:T.156 Salt bridges: C:K.155 pi-Cation interactions: C:K.127

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: D.31, H.33, H.65 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.31, A:D.31, A:H.33, A:H.65, H2O.5 ZN.4: 3 residues within 4Å: Chain B: D.31, H.33, H.65 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.31, B:D.31, B:H.33, B:H.65, H2O.10 ZN.6: 3 residues within 4Å: Chain C: D.31, H.33, H.65 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.31, C:D.31, C:H.33, C:H.65, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Begley, D.W. et al., Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei. J Struct Funct Genomics (2011)

Release Date

2008-11-04

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

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

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