SMTL ID : 5iwy.1 (1 other biounit)

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis complexed with CMP and Mg2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.9, H.11, H.43 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.9, A:H.11, A:H.43, H2O.2, H2O.3 MG.4: 3 residues within 4Å: Chain B: D.9, H.11, H.43 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.9, B:H.11, B:H.43, H2O.3, H2O.4 MG.6: 3 residues within 4Å: Chain C: D.9, H.11, H.43 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.9, C:H.11, C:H.43, H2O.5, H2O.6

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

C5P.2: 12 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.57, G.59, K.60 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:A.132, A:T.134 Hydrogen bonds: A:A.101, A:M.106, A:L.107, A:T.134, A:E.136, A:E.136, C:D.57, C:G.59, C:K.60 Water bridges: A:A.132 C5P.3: 11 residues within 4Å: Chain A: D.57, G.59 Chain B: A.101, P.104, K.105, M.106, L.107, A.132, T.133, T.134, E.136 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.132, B:T.134 Hydrogen bonds: B:A.101, B:K.105, B:M.106, B:L.107, B:T.133, B:T.134, B:E.136, B:E.136, A:D.57, A:G.59 Water bridges: B:A.132, B:T.134 C5P.5: 11 residues within 4Å: Chain B: D.57, G.59 Chain C: A.101, P.104, K.105, M.106, L.107, A.132, T.133, T.134, E.136 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:A.132, C:T.134 Hydrogen bonds: C:A.101, C:M.106, C:L.107, C:T.134, C:T.134, C:E.136, B:D.57, B:G.59 Water bridges: C:T.134, C:T.134, C:E.136, B:D.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Z.C. et al., Crystal structure of IspF from Bacillus subtilis and absence of protein complex assembly among IspD/IspE/IspF enzymes in the MEP pathway. Biosci. Rep. (2018)

Release Date

2017-03-29

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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