SMTL ID : 3ieq.1

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

3 x CTN: 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE(Non-covalent)

CTN.1: 11 residues within 4Å: Chain A: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156 Chain C: D.79, G.81, R.82 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:G.81, A:A.123, A:L.128, A:A.129 Hydrophobic interactions: A:T.156 Water bridges: A:T.156 CTN.5: 12 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 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:T.156 Hydrogen bonds: B:A.123, B:L.128, B:A.129, B:A.154, A:G.81, A:D.86 Water bridges: A:R.82, A:R.82 CTN.7: 12 residues within 4Å: Chain B: D.79, G.81, R.82 Chain C: A.123, P.126, K.127, L.128, A.129, I.132, A.154, K.155, T.156 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:T.156 Hydrogen bonds: C:A.123, C:L.128, C:A.129, C:A.154, B:G.81

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.3 ZN.6: 3 residues within 4Å: Chain B: D.31, H.33, H.65 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.31, B:H.33, B:H.65, H2O.10 ZN.8: 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.10

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 6 residues within 4Å: Chain A: Q.124, T.156, N.157, E.158, K.159, G.164 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 1 residues within 4Å: Chain B: E.170 No protein-ligand interaction detected (PLIP)

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

2009-08-04

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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