SMTL ID : 3eor.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.14, H.16, H.48 Ligands: NA.2, NA.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.14, A:H.16, A:H.48 ZN.6: 5 residues within 4Å: Chain B: D.14, H.16, H.48 Ligands: NA.7, NA.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.14, B:H.16, B:H.48 ZN.11: 5 residues within 4Å: Chain C: D.14, H.16, H.48 Ligands: NA.12, NA.13 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.14, C:H.16, C:H.48

6 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: D.14 Chain C: T.138 Ligands: ZN.1 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:T.139 Hydrogen bonds: A:D.14 NA.3: 4 residues within 4Å: Chain A: H.16, S.41, H.48 Ligands: ZN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.16, A:S.41 NA.7: 3 residues within 4Å: Chain A: T.138 Chain B: D.14 Ligands: ZN.6 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.138, B:D.14 Water bridges: A:T.139 NA.8: 4 residues within 4Å: Chain B: H.16, S.41, H.48 Ligands: ZN.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.41 NA.12: 3 residues within 4Å: Chain B: T.138 Chain C: D.14 Ligands: ZN.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.138, B:T.138 Water bridges: B:T.139 NA.13: 4 residues within 4Å: Chain C: H.16, S.41, H.48 Ligands: ZN.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.41, C:S.41

3 x CFV: [(2R)-1-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-propan-2-yl]oxymethylphosphonic acid(Non-covalent)

CFV.4: 10 residues within 4Å: Chain A: A.106, P.109, K.110, M.111, L.112, A.137, T.138, T.139 Chain B: G.64, D.69 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.139 Hydrogen bonds: A:A.106, A:M.111, A:L.112 CFV.9: 10 residues within 4Å: Chain B: A.106, P.109, K.110, M.111, L.112, A.137, T.138, T.139 Chain C: G.64, D.69 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.139 Hydrogen bonds: B:A.106, B:M.111, B:L.112 CFV.14: 10 residues within 4Å: Chain A: G.64, D.69 Chain C: A.106, P.109, K.110, M.111, L.112, A.137, T.138, T.139 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:T.139 Hydrogen bonds: C:A.106, C:M.111, C:L.112

3 x GPP: GERANYL DIPHOSPHATE(Covalent)

GPP.5: 15 residues within 4Å: Chain A: G.144, F.145, T.146, R.148, E.155 Chain B: G.144, F.145, R.148, E.155 Chain C: G.144, F.145, R.148, E.155 Ligands: GPP.10, GPP.15 11 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: C:F.145, A:F.145, B:F.145 Salt bridges: C:R.148, C:R.148, A:R.148, A:R.148, B:R.148, B:R.148 Hydrophobic interactions: A:T.146, B:F.145 GPP.10: 15 residues within 4Å: Chain A: G.144, F.145, R.148, E.155 Chain B: G.144, F.145, T.146, R.148, E.155 Chain C: G.144, F.145, R.148, E.155 Ligands: GPP.5, GPP.15 11 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: C:F.145, B:T.146 Hydrogen bonds: C:F.145, A:F.145, B:F.145 Salt bridges: C:R.148, C:R.148, A:R.148, A:R.148, B:R.148, B:R.148 GPP.15: 15 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: G.144, F.145, T.146, R.148, E.155 Ligands: GPP.5, GPP.10 11 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: C:T.146, A:F.145 Hydrogen bonds: C:F.145, A:F.145, B:F.145 Salt bridges: C:R.148, C:R.148, A:R.148, A:R.148, B: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
A

C
A

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

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