SMTL ID : 3fba.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.14, A:H.16, A:H.48 ZN.5: 3 residues within 4Å: Chain B: D.14, H.16, H.48 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.14, B:H.16, B:H.48 ZN.9: 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 C6B: [(2S,3S,4R,5S)-5-(4-amino-2-oxo-pyrimidin-1-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate(Non-covalent)

C6B.2: 12 residues within 4Å: Chain A: A.106, P.109, K.110, M.111, L.112, A.137, T.138, T.139 Chain B: D.62, I.63, G.64, D.69 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.139 Hydrogen bonds: A:A.106, A:K.110, A:M.111, A:L.112, B:D.62, B:G.64, B:G.64 C6B.6: 12 residues within 4Å: Chain B: A.106, P.109, K.110, M.111, L.112, A.137, T.138, T.139 Chain C: D.62, I.63, G.64, D.69 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:D.62, C:G.64, C:G.64, B:A.106, B:K.110, B:M.111, B:L.112, B:T.138 Hydrophobic interactions: B:T.139 C6B.10: 12 residues within 4Å: Chain A: D.62, I.63, G.64, D.69 Chain C: A.106, P.109, K.110, M.111, L.112, A.137, T.138, T.139 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:D.62, A:D.62, A:G.64, A:G.64, C:A.106, C:K.110, C:M.111, C:L.112, C:T.138 Hydrophobic interactions: C:T.139

3 x GPP: GERANYL DIPHOSPHATE(Non-covalent)

GPP.3: 17 residues within 4Å: Chain A: T.140, G.144, F.145, T.146, R.148 Chain B: F.13, G.144, F.145, R.148, E.155 Chain C: G.144, F.145, T.146, R.148, E.155 Ligands: GPP.7, GPP.11 13 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: C:F.145, C:T.146, B:F.145, A:F.145 Salt bridges: C:R.148, B:R.148, A:R.148 Hydrophobic interactions: B:F.13, B:F.13, B:F.145, A:T.140, A:F.145, A:T.146 GPP.7: 17 residues within 4Å: Chain A: G.144, F.145, T.146, R.148, E.155 Chain B: T.140, G.144, F.145, T.146, R.148 Chain C: F.13, G.144, F.145, R.148, E.155 Ligands: GPP.3, GPP.11 13 PLIP interactions: 5 interactions with chain C, 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: C:F.13, C:F.13, C:F.145, B:T.140, B:F.145, B:T.146 Hydrogen bonds: C:F.145, B:F.145, A:F.145, A:T.146 Salt bridges: C:R.148, B:R.148, A:R.148 GPP.11: 17 residues within 4Å: Chain A: F.13, G.144, F.145, R.148, E.155 Chain B: G.144, F.145, T.146, R.148, E.155 Chain C: T.140, G.144, F.145, T.146, R.148 Ligands: GPP.3, GPP.7 13 PLIP interactions: 5 interactions with chain C, 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: C:T.140, C:F.145, C:T.146, A:F.13, A:F.13, A:F.145 Hydrogen bonds: C:F.145, B:F.145, B:T.146, A:F.145 Salt bridges: C:R.148, B:R.148, A:R.148

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: H.129, M.130, D.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.130, A:D.131 GOL.8: 3 residues within 4Å: Chain B: H.129, M.130, D.131 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.130, B:D.131 GOL.12: 3 residues within 4Å: Chain C: H.129, M.130, D.131 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:M.130, C:D.131

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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