SMTL ID : 3ern.2 (1 other biounit)

Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with AraCMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: D.14, H.16, H.48 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.14, A:D.14, A:H.16, A:H.48 ZN.4: 4 residues within 4Å: Chain B: D.14, H.16, H.48 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.14, B:H.16, B:H.48

2 x CAR: CYTOSINE ARABINOSE-5'-PHOSPHATE(Non-covalent)

CAR.2: 10 residues within 4Å: Chain A: A.106, P.109, K.110, M.111, L.112, A.137, T.138, T.139 Chain C: D.62, G.64 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:T.139 Hydrogen bonds: A:A.106, A:M.111, A:L.112, A:A.137, A:T.139, A:T.139, C:D.62, C:G.64 CAR.3: 10 residues within 4Å: Chain A: D.62, G.64 Chain B: A.106, P.109, K.110, M.111, L.112, A.137, T.138, T.139 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:G.64, B:A.106, B:M.111, B:L.112, B:A.137, B:T.139 Water bridges: A:D.62, B:A.137 Hydrophobic interactions: B:T.139

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 7 residues within 4Å: Chain B: H.16, A.39, H.40, S.41, H.48, D.69 Ligands: ZN.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.40, B:S.41, B:S.41 Salt bridges: B:H.16, B:H.48

1 x GPP: GERANYL DIPHOSPHATE(Non-covalent)

GPP.6: 13 residues within 4Å: Chain A: G.144, F.145, R.148, E.155 Chain B: G.144, F.145, R.148, E.155 Chain C: F.13, G.144, F.145, R.148, E.155 11 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C, 3 interactions with chain B Hydrogen bonds: A:F.145, C:F.145, B:G.144, B:F.145 Water bridges: A:R.148, C:T.146 Salt bridges: A:R.148, C:R.148, B:R.148 Hydrophobic interactions: C:F.13, C:F.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramsden, N.L. et al., A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy. J.Med.Chem. (2009)

Release Date

2009-08-25

Peptides

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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