SMTL ID : 3ike.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.14, H.16, H.48 Chain B: K.138 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.14, A:H.16, A:H.48, H2O.6 ZN.6: 3 residues within 4Å: Chain B: D.14, H.16, H.48 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.14, B:H.16, B:H.48, H2O.8 ZN.8: 3 residues within 4Å: Chain C: D.14, H.16, H.48 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.14, C:D.14, C:H.16, C:H.48, H2O.9

3 x CYT: 6-AMINOPYRIMIDIN-2(1H)-ONE(Non-covalent)

CYT.2: 8 residues within 4Å: Chain A: A.106, P.109, K.110, L.111, A.112, A.137, K.138, T.139 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.139 Hydrogen bonds: A:P.109, A:P.109, A:L.111, A:A.112 CYT.5: 8 residues within 4Å: Chain B: A.106, P.109, K.110, L.111, A.112, A.137, K.138, T.139 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.139 Hydrogen bonds: B:A.106, B:P.109, B:L.111, B:A.112 CYT.7: 9 residues within 4Å: Chain C: A.106, Q.107, P.109, K.110, L.111, A.112, A.137, K.138, T.139 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:T.139 Hydrogen bonds: C:P.109, C:P.109, C:L.111, C:A.112

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

CL.3: 6 residues within 4Å: Chain A: Q.107, T.139, N.140, E.141, K.142, G.147 Ligand excluded by PLIP

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

MG.4: 0 residues within 4Å: (No contacts) 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

2009-08-18

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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