SMTL ID : 3q8h.1

Crystal structure of 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei in complex with cytidine derivative EBSI01028

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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: AO9.2 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.5 ZN.7: 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.9: 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.1

3 x AO9: 5'-deoxy-5'-[(imidazo[2,1-b][1,3]thiazol-5-ylcarbonyl)amino]cytidine(Non-covalent)

AO9.2: 17 residues within 4Å: Chain A: H.57, H.65, D.79, I.80, G.81, R.82, F.84, L.99 Chain B: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156 Ligands: ZN.1 12 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:T.156 Hydrogen bonds: B:A.123, B:L.128, B:A.129, B:A.154, A:D.79, A:G.81 Water bridges: B:A.154, B:K.155, A:H.57 pi-Stacking: A:H.57, A:H.65 AO9.6: 16 residues within 4Å: Chain A: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156 Chain C: H.57, H.65, D.79, I.80, G.81, R.82, F.84, L.99 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:T.156 Hydrogen bonds: A:A.123, A:L.128, A:A.129, A:A.154, C:D.79, C:G.81 pi-Stacking: C:H.57, C:H.65, C:H.65 AO9.8: 16 residues within 4Å: Chain B: H.57, H.65, D.79, I.80, G.81, R.82, F.84, L.99 Chain C: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156 14 PLIP interactions: 9 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:A.154, C:T.156 Hydrogen bonds: C:A.123, C:K.127, C:L.128, C:A.129, C:A.154, B:D.79, B:G.81 Water bridges: C:A.154, C:K.155 pi-Stacking: B:H.57, B:H.65, B:H.65

1 x K: POTASSIUM ION(Non-functional Binders)

K.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: R.101, A.104, A.141, D.142, L.143 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.101, A:A.141, A:D.144 EDO.5: 5 residues within 4Å: Chain A: A.113, I.114, L.143, D.144, L.145 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.114 Water bridges: A:I.114, A:L.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Cytidine derivatives as IspF inhibitors of Burkolderia pseudomallei. Bioorg.Med.Chem.Lett. (2013)

Release Date

2011-01-19

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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