SMTL ID : 3mbm.1

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytosine and FoL fragment 717, imidazo[2,1-b][1,3]thiazol-6-ylmethanol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.31, H.33, H.65 Ligands: 717.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.31, A:H.33, A:H.65 ZN.5: 4 residues within 4Å: Chain B: D.31, H.33, H.65 Ligands: 717.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.31, B:D.31, B:H.33, B:H.65 ZN.9: 4 residues within 4Å: Chain C: D.31, H.33, H.65 Ligands: 717.8 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.31, C:D.31, C:H.33, C:H.65

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

CYT.2: 8 residues within 4Å: Chain A: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.156 Hydrogen bonds: A:P.126, A:P.126, A:L.128, A:A.129 Water bridges: A:K.127 pi-Cation interactions: A:K.127 CYT.6: 8 residues within 4Å: Chain B: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.156 Hydrogen bonds: B:P.126, B:P.126, B:L.128, B:A.129 CYT.10: 9 residues within 4Å: Chain C: A.123, Q.124, P.126, K.127, L.128, A.129, A.154, K.155, T.156 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:T.156 Hydrogen bonds: C:P.126, C:P.126, C:L.128, C:A.129

3 x 717: imidazo[2,1-b][1,3]thiazol-6-ylmethanol(Non-covalent)

717.3: 10 residues within 4Å: Chain A: D.31, V.32, H.33, H.65, I.80, F.84, D.86 Chain B: K.155, E.158 Ligands: ZN.1 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.155, A:V.32 pi-Cation interactions: B:K.155 717.7: 9 residues within 4Å: Chain B: D.31, V.32, H.33, H.65, I.80 Chain C: K.155, T.156, E.158 Ligands: ZN.5 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:K.155, C:E.158, B:V.32 pi-Cation interactions: C:K.155 Water bridges: B:V.32 717.8: 11 residues within 4Å: Chain A: K.155, T.156, E.158 Chain C: D.31, V.32, H.33, H.65, I.80, F.84, D.86 Ligands: ZN.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.155, A:T.156, A:E.158 pi-Cation interactions: A:K.155

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 8 residues within 4Å: Chain A: Y.30, E.170, Q.172 Chain B: Y.30, E.170, Q.172 Chain C: E.170, Q.172 6 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:Q.172, B:E.170, B:Q.172, C:Q.172 Water bridges: A:Y.162, A:E.170

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

2010-04-07

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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