SMTL ID : 4c81.1

IspF (Plasmodium falciparum) CDP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-trimer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.15, H.17, H.67 Ligands: CDP.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.15, A:D.15, A:H.17, A:H.67, H2O.1 ZN.2: 5 residues within 4Å: Chain A: H.159 Chain B: Y.14, E.172 Ligands: CL.4, CL.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:E.172, A:H.159 ZN.8: 4 residues within 4Å: Chain B: D.15, H.17, H.67 Ligands: CDP.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.15, B:D.15, B:H.17, B:H.67, H2O.4 ZN.9: 5 residues within 4Å: Chain B: H.159 Chain C: Y.14, E.172 Ligands: CL.11, CL.13 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Metal complexes: C:E.172, B:H.159 ZN.15: 4 residues within 4Å: Chain C: D.15, H.17, H.67 Ligands: CDP.17 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.15, C:D.15, C:H.17, C:H.67, H2O.7 ZN.16: 5 residues within 4Å: Chain A: Y.14, E.172 Chain C: H.159 Ligands: CL.18, CL.20 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Metal complexes: A:E.172, C:H.159

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

CDP.3: 15 residues within 4Å: Chain A: D.15, H.17, D.81, G.83, T.84 Chain C: A.125, P.128, K.129, I.130, S.131, G.156, K.157, T.158, E.160 Ligands: ZN.1 18 PLIP interactions: 4 interactions with chain A, 14 interactions with chain C Hydrogen bonds: A:D.81, A:G.83, C:A.125, C:I.130, C:S.131, C:T.158, C:T.158 Water bridges: A:H.17, C:S.131, C:R.134, C:G.156, C:K.157, C:K.157, C:E.160 Salt bridges: A:H.17, C:K.157, C:K.157 Hydrophobic interactions: C:T.158 CDP.10: 15 residues within 4Å: Chain A: A.125, P.128, K.129, I.130, S.131, G.156, K.157, T.158, E.160 Chain B: D.15, H.17, D.81, G.83, T.84 Ligands: ZN.8 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.158 Hydrogen bonds: A:A.125, A:I.130, A:S.131, A:T.158, A:T.158, B:D.81, B:G.83 Water bridges: A:S.131, A:R.134, A:G.156, A:K.157, A:K.157, A:E.160, A:E.160 Salt bridges: A:K.157, A:K.157, B:H.17 CDP.17: 15 residues within 4Å: Chain B: A.125, P.128, K.129, I.130, S.131, G.156, K.157, T.158, E.160 Chain C: D.15, H.17, D.81, G.83, T.84 Ligands: ZN.15 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:T.158 Hydrogen bonds: B:A.125, B:I.130, B:S.131, B:T.158, B:T.158, C:D.81, C:G.83 Water bridges: B:S.131, B:R.134, B:G.156, B:K.157, B:K.157, B:E.160, B:E.160 Salt bridges: B:K.157, B:K.157, C:H.17

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

CL.4: 6 residues within 4Å: Chain A: H.159 Chain B: V.164, I.165, E.172 Ligands: ZN.2, CL.6 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: H.17, K.18, L.57, S.58 Chain C: E.160 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: H.159, E.172 Chain B: Y.14, E.172 Ligands: ZN.2, CL.4 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain B: H.159 Chain C: V.164, I.165, E.172 Ligands: ZN.9, CL.13 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: E.160 Chain B: H.17, K.18, L.57, S.58 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain B: H.159, E.172 Chain C: Y.14, E.172 Ligands: ZN.9, CL.11 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain A: V.164, I.165, E.172 Chain C: H.159 Ligands: ZN.16, CL.20 Ligand excluded by PLIP CL.19: 5 residues within 4Å: Chain B: E.160 Chain C: H.17, K.18, L.57, S.58 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain A: Y.14, E.172 Chain C: H.159, E.172 Ligands: ZN.16, CL.18 Ligand excluded by PLIP

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

SO4.7: 8 residues within 4Å: Chain A: G.163, V.164 Chain B: G.163, V.164 Chain C: G.163, V.164 Ligands: SO4.14, SO4.21 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:V.164, C:V.164, B:V.164 Water bridges: A:I.165, B:I.165 SO4.14: 8 residues within 4Å: Chain A: G.163, V.164 Chain B: G.163, V.164 Chain C: G.163, V.164 Ligands: SO4.7, SO4.21 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:V.164, C:V.164, B:V.164 Water bridges: C:I.165, B:I.165 SO4.21: 8 residues within 4Å: Chain A: G.163, V.164 Chain B: G.163, V.164 Chain C: G.163, V.164 Ligands: SO4.7, SO4.14 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:V.164, B:V.164, A:V.164 Water bridges: C:I.165, A:I.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

O Rourke, P.E. et al., Crystal Structures of Ispf from Plasmodium Falciparum and Burkholderia Cenocepacia: Comparisons Inform Antimicrobial Drug Target Assessment. Bmc Struct.Biol. (2014)

Release Date

2014-01-08

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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