SMTL ID : 3esj.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 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: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.14, A:H.16, A:H.48, H2O.1 ZN.5: 3 residues within 4Å: Chain B: D.14, H.16, H.48 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.14, B:H.16, B:H.48, H2O.5 ZN.9: 3 residues within 4Å: Chain C: D.14, H.16, H.48 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.14, C:H.16, C:H.48, H2O.9

3 x CC7: 4-amino-1-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxidotetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]pyrimidin-2(1H)-one(Non-covalent)

CC7.2: 12 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, I.63, G.64, D.69 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:D.62, C:G.64, A:A.106, A:K.110, A:M.111, A:L.112 Water bridges: C:D.69, A:A.137 Hydrophobic interactions: A:A.137, A:T.139 CC7.6: 12 residues within 4Å: Chain A: D.62, I.63, G.64, D.69 Chain B: A.106, P.109, K.110, M.111, L.112, A.137, T.138, T.139 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.137, B:T.139 Hydrogen bonds: B:A.106, B:K.110, B:M.111, B:L.112, A:D.62, A:G.64 Water bridges: B:A.137, A:D.69 CC7.10: 12 residues within 4Å: Chain B: 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 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:A.137, C:T.139 Hydrogen bonds: C:A.106, C:K.110, C:M.111, C:L.112, B:D.62, B:G.64 Water bridges: C:A.137, B:D.62, B:D.62, B:D.69

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: E.155 Chain B: E.155 Chain C: E.155 Ligands: MG.7, MG.11 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Metal complexes: A:E.155, A:E.155, B:E.155, C:E.155, C:E.155 MG.7: 5 residues within 4Å: Chain A: E.155 Chain B: E.155 Chain C: E.155 Ligands: MG.3, MG.11 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C Metal complexes: A:E.155, A:E.155, B:E.155, B:E.155, C:E.155 MG.11: 5 residues within 4Å: Chain A: E.155 Chain B: E.155 Chain C: E.155 Ligands: MG.3, MG.7 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 interactions with chain C Metal complexes: A:E.155, B:E.155, B:E.155, C:E.155, C:E.155

3 x GPP: GERANYL DIPHOSPHATE(Non-covalent)

GPP.4: 18 residues within 4Å: Chain A: F.13, I.105, T.140, L.143, G.144, F.145, T.146, R.148, E.155 Chain B: G.144, F.145, R.148 Chain C: F.13, G.144, F.145, R.148 Ligands: GPP.8, GPP.12 13 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: A:F.13, A:I.105, A:F.145, A:T.146, A:E.155, C:F.13, C:F.145 Hydrogen bonds: A:F.145, B:F.145, C:F.145 Salt bridges: A:R.148, B:R.148, C:R.148 GPP.8: 18 residues within 4Å: Chain A: F.13, G.144, F.145, R.148 Chain B: F.13, I.105, T.140, L.143, G.144, F.145, T.146, R.148, E.155 Chain C: G.144, F.145, R.148 Ligands: GPP.4, GPP.12 13 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: A:F.13, A:F.145, B:F.13, B:I.105, B:F.145, B:T.146, B:E.155 Hydrogen bonds: A:F.145, B:F.145, C:F.145 Salt bridges: A:R.148, B:R.148, C:R.148 GPP.12: 18 residues within 4Å: Chain A: G.144, F.145, R.148 Chain B: F.13, G.144, F.145, R.148 Chain C: F.13, I.105, T.140, L.143, G.144, F.145, T.146, R.148, E.155 Ligands: GPP.4, GPP.8 13 PLIP interactions: 2 interactions with chain A, 7 interactions with chain C, 4 interactions with chain B Hydrogen bonds: A:F.145, C:F.145, B:F.145 Salt bridges: A:R.148, C:R.148, B:R.148 Hydrophobic interactions: C:F.13, C:I.105, C:F.145, C:T.146, C:E.155, B:F.13, B: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
A

B
A

C
A

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

Related Entries With Identical Sequence