SMTL ID : 3elc.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

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

3 x F01: 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-fluoro-pyrimidin-2-one(Non-covalent)

F01.2: 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 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:A.106, A:K.110, A:M.111, A:L.112, C:G.64 Water bridges: A:A.137 F01.4: 11 residues within 4Å: Chain A: D.62, I.63, G.64 Chain B: A.106, P.109, K.110, M.111, L.112, A.137, T.138, T.139 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.106, B:M.111, B:L.112, A:G.64 pi-Cation interactions: B:K.110 F01.6: 10 residues within 4Å: Chain B: D.62, G.64 Chain C: A.106, P.109, K.110, M.111, L.112, A.137, T.138, T.139 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.106, C:K.110, C:M.111, C:L.112 Water bridges: C:A.137

1 x GPP: GERANYL DIPHOSPHATE(Non-covalent)

GPP.7: 10 residues within 4Å: Chain A: G.144, F.145, R.148 Chain B: G.144, F.145, R.148 Chain C: T.140, G.144, F.145, R.148 12 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: C:T.140, B:F.145 Hydrogen bonds: C:G.144, C:F.145, A:G.144, A:F.145, B:F.145 Water bridges: C:R.148, C:R.148 Salt bridges: C:R.148, A:R.148, B:R.148

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
A

B
B

C
C

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

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