SMTL ID : 1iv4.1 (1 other biounit)

Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form Substrate)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-trimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.8, H.10, H.42 Ligands: MG.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.8, A:D.8, A:H.10, A:H.42, H2O.1 MG.2: 4 residues within 4Å: Chain A: D.8 Chain C: K.132 Ligands: MG.1, C5P.9 5 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.8, H2O.1, H2O.2, H2O.9, C5P.9 MG.3: 4 residues within 4Å: Chain A: K.132 Chain B: D.8 Ligands: C5P.4, MG.5 5 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:D.8, H2O.2, H2O.5, H2O.6, C5P.4 MG.5: 4 residues within 4Å: Chain B: D.8, H.10, H.42 Ligands: MG.3 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.8, B:D.8, B:H.10, B:H.42, H2O.5 MG.6: 4 residues within 4Å: Chain B: K.132 Chain C: D.8 Ligands: C5P.7, MG.8 5 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:D.8, H2O.6, H2O.9, H2O.9, C5P.7 MG.8: 4 residues within 4Å: Chain C: D.8, H.10, H.42 Ligands: MG.6 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.8, C:D.8, C:H.10, C:H.42, H2O.9

3 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.4: 15 residues within 4Å: Chain A: L.100, P.103, K.104, L.105, G.106, R.109, F.131, K.132, T.133, E.135 Chain B: D.56, I.57, G.58, L.59 Ligands: MG.3 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.133 Hydrogen bonds: A:L.100, A:L.105, A:G.106, A:R.109, A:T.133, A:E.135, A:E.135, B:D.56, B:G.58 Water bridges: A:K.132, A:K.132, A:K.132, A:K.132, A:K.132 Salt bridges: A:K.132 C5P.7: 14 residues within 4Å: Chain B: L.100, P.103, K.104, L.105, G.106, R.109, F.131, K.132, T.133, E.135 Chain C: D.56, I.57, G.58 Ligands: MG.6 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:T.133 Hydrogen bonds: B:L.100, B:L.105, B:G.106, B:R.109, B:T.133, B:E.135, B:E.135, C:D.56, C:G.58 Water bridges: B:K.132 Salt bridges: B:K.132 C5P.9: 15 residues within 4Å: Chain A: D.56, I.57, G.58, L.59 Chain C: L.100, P.103, K.104, L.105, G.106, R.109, F.131, K.132, T.133, E.135 Ligands: MG.2 17 PLIP interactions: 10 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:T.133 Hydrogen bonds: C:L.100, C:L.105, C:G.106, C:R.109, C:T.133, C:E.135, A:D.56, A:G.58 Water bridges: C:K.132, C:E.135, A:D.8, A:D.8, A:D.8, A:D.8, A:H.10 Salt bridges: C:K.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kishida, H. et al., Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis. Acta Crystallogr.,Sect.D (2003)

Release Date

2002-09-11

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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