SMTL ID : 3fpi.1

Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase IspF complexed with Cytidine Triphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-trimer

Ligands

3 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.1: 19 residues within 4Å: Chain A: D.11, H.13, A.38, H.39, S.40, H.47, D.61, G.63, D.68 Chain C: A.105, P.108, K.109, M.110, A.111, A.136, T.137, T.138, E.140 Ligands: MG.5 16 PLIP interactions: 5 interactions with chain C, 11 interactions with chain A Hydrogen bonds: C:A.105, C:A.111, C:T.138, C:T.138, A:D.11, A:H.39, A:S.40, A:D.61, A:G.63, A:D.68 Water bridges: C:A.136, A:H.47, A:H.47 Salt bridges: A:H.13, A:H.13, A:H.47 CTP.7: 19 residues within 4Å: Chain A: A.105, P.108, K.109, M.110, A.111, A.136, T.137, T.138, E.140 Chain B: D.11, H.13, A.38, H.39, S.40, H.47, D.61, G.63, D.68 Ligands: MG.11 17 PLIP interactions: 6 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:A.105, A:A.111, A:T.137, A:T.138, A:T.138, B:D.11, B:H.39, B:S.40, B:D.61, B:G.63, B:D.68 Water bridges: A:A.136, B:H.47, B:H.47 Salt bridges: B:H.13, B:H.13, B:H.47 CTP.13: 19 residues within 4Å: Chain B: A.105, P.108, K.109, M.110, A.111, A.136, T.137, T.138, E.140 Chain C: D.11, H.13, A.38, H.39, S.40, H.47, D.61, G.63, D.68 Ligands: MG.17 16 PLIP interactions: 5 interactions with chain B, 11 interactions with chain C Hydrogen bonds: B:A.105, B:A.111, B:T.138, B:T.138, C:D.11, C:H.39, C:S.40, C:D.61, C:G.63, C:D.68 Water bridges: B:A.136, C:H.47, C:H.47 Salt bridges: C:H.13, C:H.13, C:H.47

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 4 residues within 4Å: Chain A: P.22, R.29, P.31, Y.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.29, A:E.33 EPE.8: 4 residues within 4Å: Chain B: P.22, R.29, P.31, Y.32 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.29, B:E.33 EPE.14: 4 residues within 4Å: Chain C: P.22, R.29, P.31, Y.32 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.29, C:E.33

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 8 residues within 4Å: Chain A: R.147 Chain B: R.147 Chain C: R.147 Ligands: MG.6, CL.9, MG.12, CL.15, MG.18 Ligand excluded by PLIP CL.9: 8 residues within 4Å: Chain A: R.147 Chain B: R.147 Chain C: R.147 Ligands: CL.3, MG.6, MG.12, CL.15, MG.18 Ligand excluded by PLIP CL.15: 8 residues within 4Å: Chain A: R.147 Chain B: R.147 Chain C: R.147 Ligands: CL.3, MG.6, CL.9, MG.12, MG.18 Ligand excluded by PLIP

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

SO4.4: 1 residues within 4Å: Chain A: R.83 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.83 SO4.10: 1 residues within 4Å: Chain B: R.83 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.83 SO4.16: 1 residues within 4Å: Chain C: R.83 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.83

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.5: 6 residues within 4Å: Chain A: A.38, H.39, S.40, G.42, H.47 Ligands: CTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.40 MG.6: 5 residues within 4Å: Ligands: CL.3, CL.9, MG.12, CL.15, MG.18 No protein-ligand interaction detected (PLIP) MG.11: 6 residues within 4Å: Chain B: A.38, H.39, S.40, G.42, H.47 Ligands: CTP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.40 MG.12: 5 residues within 4Å: Ligands: CL.3, MG.6, CL.9, CL.15, MG.18 No protein-ligand interaction detected (PLIP) MG.17: 6 residues within 4Å: Chain C: A.38, H.39, S.40, G.42, H.47 Ligands: CTP.13 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.40 MG.18: 5 residues within 4Å: Ligands: CL.3, MG.6, CL.9, MG.12, CL.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase IspF complexed with Cytidine Triphosphate. To be Published

Release Date

2009-02-03

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

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