SMTL ID : 2uzh.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.13, H.15, H.47 Ligands: CDP.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.13, A:H.15, A:H.47 ZN.5: 4 residues within 4Å: Chain C: D.13, H.15, H.47 Ligands: CDP.6 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.13, C:D.13, C:H.15, C:H.47 ZN.11: 4 residues within 4Å: Chain B: D.13, H.15, H.47 Ligands: CDP.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.13, B:D.13, B:H.15, B:H.47

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

CDP.2: 16 residues within 4Å: Chain A: G.105, N.106, P.108, K.109, V.110, G.111, A.133, T.134, T.135 Chain B: T.12, D.13, V.14, H.15, D.61, G.63 Ligands: ZN.11 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:A.133, A:T.135 Hydrogen bonds: A:G.105, A:V.110, A:G.111, A:T.135, B:D.13, B:D.13, B:V.14, B:D.61, B:G.63 Water bridges: A:A.133, A:A.133, A:D.137, B:L.62 pi-Cation interactions: A:K.109 Salt bridges: B:H.15 CDP.6: 16 residues within 4Å: Chain B: G.105, N.106, P.108, K.109, V.110, G.111, A.133, T.134, T.135 Chain C: D.13, V.14, H.15, D.61, L.62, G.63 Ligands: ZN.5 15 PLIP interactions: 7 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:T.135 Hydrogen bonds: B:G.105, B:V.110, B:G.111, B:T.134, B:T.135, B:T.135, C:D.13, C:D.13, C:V.14, C:D.61, C:G.63, C:T.64 Water bridges: C:L.62 Salt bridges: C:H.15 CDP.12: 16 residues within 4Å: Chain A: D.13, H.15, D.61, L.62, G.63 Chain C: G.105, N.106, P.108, K.109, V.110, G.111, A.133, T.134, T.135, D.137 Ligands: ZN.1 17 PLIP interactions: 4 interactions with chain A, 13 interactions with chain C Hydrogen bonds: A:D.61, A:G.63, C:G.105, C:V.110, C:G.111, C:T.134, C:T.135, C:T.135 Water bridges: A:D.51, A:L.62, C:A.133, C:A.133, C:T.135, C:T.135 Hydrophobic interactions: C:A.133, C:T.135 pi-Cation interactions: C:K.109

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 10 residues within 4Å: Chain A: R.114, Q.118, S.130, V.131, S.132 Chain B: L.54, S.55, G.58, L.59, G.60 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.58, B:G.60, A:R.114, A:Q.118, A:S.132 Water bridges: B:S.55 EDO.13: 10 residues within 4Å: Chain A: L.54, S.55, G.58, L.59, G.60 Chain C: R.114, Q.118, S.130, V.131, S.132 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:R.114, C:Q.118, C:Q.118, C:S.132, A:G.60 Water bridges: A:S.55, A:S.55

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: Q.118, P.128, V.129, S.130 Chain B: R.7, G.58 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.7, B:R.7, A:S.122, A:S.122, A:S.130 Water bridges: B:A.57, A:S.130 GOL.8: 3 residues within 4Å: Chain B: P.16, I.17, E.18 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.18 GOL.14: 3 residues within 4Å: Chain C: G.126, A.127 Ligands: ACT.15 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.86, C:R.86, C:I.96, C:A.127

1 x IPE: 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

IPE.7: 10 residues within 4Å: Chain A: G.140, L.141, R.144 Chain B: T.136, G.140, L.141, R.144, A.149 Chain C: G.140, L.141 12 PLIP interactions: 4 interactions with chain C, 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: C:L.141, C:L.141, B:T.136, B:A.149 Hydrogen bonds: C:L.141, B:L.141, A:L.141 Water bridges: C:L.141, B:R.144, A:R.144 Salt bridges: B:R.144, A:R.144

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 5 residues within 4Å: Chain B: C.27, A.79, R.83, V.120, L.124 2 PLIP interactions: 2 interactions with chain B Water bridges: B:C.27, B:S.77 PEG.10: 5 residues within 4Å: Chain B: G.20, R.21, D.32, A.33, D.34 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.21, B:A.33 Water bridges: B:D.32, B:R.107

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.15: 4 residues within 4Å: Chain C: R.86, E.123, G.126 Ligands: GOL.14 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.123 Water bridges: C:R.86 Salt bridges: C:R.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buetow, L. et al., The Structure of Mycobacteria 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase, an Essential Enzyme, Provides a Platform for Drug Discovery. Bmc Struct.Biol. (2007)

Release Date

2007-11-06

Peptides

2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE