SMTL ID : 1jy8.1

2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.8, H.10, H.42 Ligands: CDI.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.8, A:D.8, A:H.10, A:H.42 ZN.4: 4 residues within 4Å: Chain B: D.8, H.10, H.42 Ligands: CDI.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.8, B:D.8, B:H.10, B:H.42 ZN.7: 4 residues within 4Å: Chain C: D.8, H.10, H.42 Ligands: CDI.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.8, C:D.8, C:H.10, C:H.42

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

C5P.2: 14 residues within 4Å: Chain A: D.56, G.58, K.59, D.63 Chain B: A.100, P.103, K.104, M.105, L.106, A.131, T.132, T.133, E.135 Ligands: CDI.3 15 PLIP interactions: 3 interactions with chain A, 12 interactions with chain B Hydrogen bonds: A:D.56, A:G.58, A:K.59, B:A.100, B:K.104, B:M.105, B:L.106, B:A.131, B:T.133, B:T.133, B:E.135 Hydrophobic interactions: B:T.133 Water bridges: B:T.132, B:E.135 pi-Cation interactions: B:K.104 C5P.5: 14 residues within 4Å: Chain B: D.56, G.58, K.59, D.63 Chain C: A.100, P.103, K.104, M.105, L.106, A.131, T.132, T.133, E.135 Ligands: CDI.6 15 PLIP interactions: 3 interactions with chain B, 12 interactions with chain C Hydrogen bonds: B:D.56, B:G.58, B:K.59, C:A.100, C:K.104, C:M.105, C:L.106, C:A.131, C:T.133, C:T.133, C:E.135 Hydrophobic interactions: C:T.133 Water bridges: C:T.132, C:E.135 pi-Cation interactions: C:K.104 C5P.8: 14 residues within 4Å: Chain A: A.100, P.103, K.104, M.105, L.106, A.131, T.132, T.133, E.135 Chain C: D.56, G.58, K.59, D.63 Ligands: CDI.9 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:T.133 Hydrogen bonds: A:A.100, A:K.104, A:M.105, A:L.106, A:A.131, A:T.133, A:T.133, A:E.135, C:D.56, C:G.58, C:K.59 Water bridges: A:T.132, A:E.135 pi-Cation interactions: A:K.104

3 x CDI: 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE(Non-covalent)

CDI.3: 17 residues within 4Å: Chain A: D.8, H.10, A.33, H.34, S.35, G.37, H.42, I.57, G.58, F.61, P.62, D.63, F.68, L.76 Chain B: E.135 Ligands: ZN.1, C5P.2 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.57, A:L.76 Hydrogen bonds: A:H.34, A:S.35, A:F.61, A:P.62, A:D.63 Water bridges: A:H.10, A:H.10, A:D.63, A:D.63, B:T.132, B:T.133 Salt bridges: A:H.10, A:H.10, A:H.42, A:H.42 CDI.6: 17 residues within 4Å: Chain B: D.8, H.10, A.33, H.34, S.35, G.37, H.42, I.57, G.58, F.61, P.62, D.63, F.68, L.76 Chain C: E.135 Ligands: ZN.4, C5P.5 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.57, B:L.76 Hydrogen bonds: B:H.34, B:S.35, B:F.61, B:P.62, B:D.63 Water bridges: B:H.10, B:H.10, B:D.63, B:D.63, C:T.132, C:T.133 Salt bridges: B:H.10, B:H.10, B:H.42, B:H.42 CDI.9: 17 residues within 4Å: Chain A: E.135 Chain C: D.8, H.10, A.33, H.34, S.35, G.37, H.42, I.57, G.58, F.61, P.62, D.63, F.68, L.76 Ligands: ZN.7, C5P.8 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.57, C:L.76 Hydrogen bonds: C:H.34, C:S.35, C:F.61, C:P.62, C:D.63 Water bridges: C:H.10, C:H.10, C:D.63, C:D.63, A:T.132, A:T.133 Salt bridges: C:H.10, C:H.10, C:H.42, C:H.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steinbacher, S. et al., Structure of 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase involved in mevalonate-independent biosynthesis of isoprenoids. J.Mol.Biol. (2002)

Release Date

2002-01-30

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

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

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