SMTL ID : 1gx1.1

Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.9, H.11, H.43 Ligands: CDP.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.9, A:H.11, A:H.43 ZN.6: 4 residues within 4Å: Chain B: D.9, H.11, H.43 Ligands: CDP.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.9, B:H.11, B:H.43 ZN.10: 4 residues within 4Å: Chain C: D.9, H.11, H.43 Ligands: CDP.2 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.9, C:H.11, C:H.43

3 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.2: 18 residues within 4Å: Chain A: A.101, P.104, K.105, M.106, L.107, A.132, T.133, T.134, E.136 Chain C: D.9, H.11, H.43, D.57, I.58, G.59, K.60 Ligands: MN.3, ZN.10 14 PLIP interactions: 5 interactions with chain C, 9 interactions with chain A Hydrogen bonds: C:D.57, C:G.59, C:K.60, A:A.101, A:L.107, A:T.134 Salt bridges: C:H.11, C:H.43 Hydrophobic interactions: A:A.132, A:T.134 Water bridges: A:K.105, A:K.105, A:T.134, A:T.134 CDP.4: 18 residues within 4Å: Chain A: D.9, H.11, H.43, D.57, G.59, K.60, D.64 Chain B: A.101, P.104, K.105, M.106, L.107, A.132, T.133, T.134, E.136 Ligands: ZN.1, MN.5 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.57, A:G.59, B:A.101, B:L.107, B:T.133, B:T.134 Water bridges: A:D.64 Salt bridges: A:H.11, A:H.43 Hydrophobic interactions: B:A.132, B:T.134 CDP.7: 17 residues within 4Å: Chain B: D.9, H.11, H.43, D.57, I.58, G.59 Chain C: A.101, P.104, K.105, M.106, L.107, A.132, T.133, T.134, E.136 Ligands: ZN.6, MN.8 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:A.132, C:T.134 Hydrogen bonds: C:A.101, C:L.107, C:T.133, C:T.134, B:D.57, B:G.59 Water bridges: C:K.105 Salt bridges: B:H.11, B:H.43

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 3 residues within 4Å: Chain A: E.136 Chain C: H.35 Ligands: CDP.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.136, H2O.4, H2O.4, H2O.4 MN.5: 2 residues within 4Å: Chain B: E.136 Ligands: CDP.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.136, H2O.8, H2O.8, H2O.8 MN.8: 2 residues within 4Å: Chain C: E.136 Ligands: CDP.7 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.136, H2O.8, H2O.8

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

SO4.9: 8 residues within 4Å: Chain A: G.139, R.143 Chain B: G.139, F.140, R.143 Chain C: G.139, F.140, R.143 9 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B, 4 interactions with chain C Hydrogen bonds: A:F.140, B:F.140, C:G.139, C:F.140 Salt bridges: A:R.143, B:R.143, C:R.143 Water bridges: B:R.143, C:R.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kemp, L.E. et al., Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase: An Essential Enzyme for Isoprenoid Biosynthesis and Target for Antimicrobial Drug Development. Proc.Natl.Acad.Sci.USA (2002)

Release Date

2002-04-03

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