SMTL ID : 3f0g.1 (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 ZN: ZINC ION(Non-covalent)

ZN.1: 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.7 ZN.3: 3 residues within 4Å: Chain B: D.31, H.33, H.65 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.31, B:D.31, B:H.33, B:H.65 ZN.5: 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.11

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

C5P.2: 12 residues within 4Å: Chain A: D.79, G.81, D.86 Chain B: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156, E.158 15 PLIP interactions: 13 interactions with chain B, 2 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, A:D.79, A:G.81 Water bridges: B:K.155, B:K.155, B:K.155, B:K.155, B:E.158 Salt bridges: B:K.155 C5P.4: 12 residues within 4Å: Chain B: D.79, G.81, R.82 Chain C: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156, E.158 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:T.156 Hydrogen bonds: C:A.123, C:L.128, C:A.129, C:T.156, C:E.158, B:D.79, B:G.81, B:R.82 Water bridges: C:K.155, B:I.80 Salt bridges: C:K.155

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
A

B
B

C
C

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

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