SMTL ID : 3qhd.1

Crystal structure of 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE Synthase from BURKHOLDERIA PSEUDOMALLEI bound to CYTIDINE, FOL795 and FOL955

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 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: MSR.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.31, A:H.33, A:H.65 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.11 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.7

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

CL.2: 6 residues within 4Å: Chain A: H.33, G.56, H.57, S.58, H.65 Ligands: MSR.4 Ligand excluded by PLIP

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

CTN.3: 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 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:G.81, A:P.126, A:L.128, A:A.129, A:A.154 Water bridges: C:G.81, A:K.155, A:T.156 Hydrophobic interactions: A:T.156 CTN.8: 12 residues within 4Å: Chain A: D.79, I.80, G.81 Chain B: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156 Ligands: MSR.4 9 PLIP interactions: 4 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, A:G.81, A:R.82 Water bridges: A:D.79, A:D.79, A:I.80 CTN.10: 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 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:G.81, C:A.123, C:L.128, C:A.129, C:A.154 Hydrophobic interactions: C:T.156 Water bridges: C:K.127, C:K.155, C:T.156

1 x MSR: 4-(1H-IMIDAZOL-1-YL)PHENOL(Non-covalent)

MSR.4: 14 residues within 4Å: Chain A: D.31, H.33, H.65, I.80, G.81, F.84, S.85, D.86, F.91 Chain B: K.155, E.158 Ligands: ZN.1, CL.2, CTN.8 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.80, A:D.86, A:F.91 Hydrogen bonds: A:F.84, A:D.86, B:K.155 pi-Cation interactions: B:K.155

1 x 795: 2-(pyridin-3-yl)-1,3-thiazole-4-carbaldehyde(Non-covalent)

795.5: 8 residues within 4Å: Chain A: H.83, F.84, D.88, R.90, A.94, A.98, L.99, R.106 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.90, A:A.94, A:L.99 Hydrogen bonds: A:R.106, A:R.106 Water bridges: A:R.90, A:R.90 pi-Stacking: A:F.84

1 x K: POTASSIUM ION(Non-covalent)

K.6: 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

2011-02-09

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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