SMTL ID : 3f0f.1

Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with hydrolyzed CDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

homo-trimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: D.31, H.33, H.65 Chain B: K.155 Ligands: ZN.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.155

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: D.31, H.33, H.65 Ligands: GOL.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.31, A:D.31, A:H.33, A:H.65 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.8 ZN.6: 3 residues within 4Å: Chain C: D.31, H.33, H.65 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.31, C:H.33, C:H.65, H2O.2

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

C5P.5: 11 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, E.158 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:A.154, 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, C:K.155, C:T.156, B:I.80 Salt bridges: C:K.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Combining functional and structural genomics to sample the essential Burkholderia structome. Plos One (2013)

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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