SMTL ID : 3iew.1

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with bound CTP and CDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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: CTP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.31, A:H.33, A:H.65 ZN.4: 4 residues within 4Å: Chain B: D.31, H.33, H.65 Ligands: CDP.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.31, B:H.33, B:H.65 ZN.7: 4 residues within 4Å: Chain C: D.31, H.33, H.65 Ligands: CDP.2 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.31, C:H.33, C:H.65

2 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.2: 15 residues within 4Å: Chain A: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156, E.158 Chain C: D.31, H.33, D.79, G.81, R.82 Ligands: ZN.7 11 PLIP interactions: 3 interactions with chain C, 8 interactions with chain A Hydrogen bonds: C:D.79, C:G.81, A:A.123, A:L.128, A:A.129, A:T.156, A:T.156 Salt bridges: C:H.33, A:K.155, A:K.155 Hydrophobic interactions: A:T.156 CDP.6: 16 residues within 4Å: Chain B: D.31, H.33, D.79, I.80, G.81, R.82 Chain C: A.123, P.126, K.127, L.128, A.129, A.154, K.155, T.156, E.158 Ligands: ZN.4 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:T.156 Hydrogen bonds: C:A.123, C:K.127, C:L.128, C:A.129, C:T.156, C:T.156, B:D.79, B:G.81 Water bridges: C:A.154 Salt bridges: C:K.155, C:K.155, B:H.33

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.3: 20 residues within 4Å: Chain A: D.31, H.33, G.56, H.57, S.58, H.65, D.79, I.80, G.81, R.82, D.86 Chain B: A.123, P.126, L.128, A.129, A.154, K.155, T.156, E.158 Ligands: ZN.1 23 PLIP interactions: 12 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:H.57, A:S.58, A:D.79, A:G.81, A:R.82, B:A.123, B:L.128, B:A.129, B:T.156, B:T.156, B:E.158 Water bridges: A:V.32, A:D.79, A:D.79, A:G.81, B:K.127, B:A.154 Salt bridges: A:H.33, A:H.33, A:H.65, B:K.155, B:K.155 Hydrophobic interactions: B:T.156

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: Y.30, E.170 Chain B: Y.30, L.163, E.170 Chain C: E.170 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.170 Water bridges: C:E.170, C:E.170, A:N.157

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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