SMTL ID : 5qpg.1

PanDDA analysis group deposition -- Crystal Structure of T. cruzi FPPS in complex with FMOPL000291a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: G.49, K.50, Y.51, F.52, R.53, Q.93 Ligands: SO4.9 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.50, A:Y.51, A:F.52 Water bridges: A:R.53, A:R.53, A:R.53, A:E.90, A:R.110, A:R.110, A:R.110 Salt bridges: A:R.53 SO4.2: 2 residues within 4Å: Chain A: Q.23, H.143 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.23 Water bridges: A:K.27, A:W.142, A:H.143, A:H.143, B:K.160 Salt bridges: A:K.27, A:H.143 SO4.8: 7 residues within 4Å: Chain A: D.172, K.209, Q.249, D.252, K.275 Ligands: ZN.4, AWV.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.249 Water bridges: A:K.209, A:K.209, A:K.209 Salt bridges: A:K.209, A:K.275 SO4.9: 7 residues within 4Å: Chain A: K.50, F.52, Y.215, F.248, T.359, R.362 Ligands: SO4.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.53, A:T.359 Water bridges: A:R.53 Salt bridges: A:K.50, A:R.362 SO4.10: 7 residues within 4Å: Chain B: G.49, K.50, Y.51, F.52, R.53, Q.93 Ligands: SO4.18 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.50, B:Y.51, B:F.52 Water bridges: B:R.53, B:R.53, B:R.53, B:E.90, B:R.110, B:R.110, B:R.110 Salt bridges: B:R.53 SO4.11: 2 residues within 4Å: Chain B: Q.23, H.143 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.23 Water bridges: B:K.27, B:W.142, B:H.143, A:K.160 Salt bridges: B:K.27, B:H.143 SO4.17: 7 residues within 4Å: Chain B: D.172, K.209, Q.249, D.252, K.275 Ligands: ZN.13, AWV.15 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.249 Water bridges: B:D.172, B:K.209, B:K.209, B:K.209, B:D.252, B:D.252, B:D.252, B:D.252, B:D.252, B:D.253, B:D.270 Salt bridges: B:K.209, B:K.275 SO4.18: 7 residues within 4Å: Chain B: K.50, F.52, Y.215, F.248, T.359, R.362 Ligands: SO4.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.53, B:T.359 Water bridges: B:R.53 Salt bridges: B:K.50, B:R.362

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

ACT.3: 2 residues within 4Å: Chain A: R.239, E.333 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.333 Salt bridges: A:R.239 ACT.12: 2 residues within 4Å: Chain B: R.239, E.333 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.333 Salt bridges: B:R.239

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 2 residues within 4Å: Chain A: D.252 Ligands: SO4.8 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.252, H2O.2, H2O.3, H2O.4, H2O.8 ZN.5: 2 residues within 4Å: Chain A: D.100, D.104 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.100, A:D.104, H2O.3, H2O.4, H2O.5 ZN.13: 2 residues within 4Å: Chain B: D.252 Ligands: SO4.17 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.252, H2O.15, H2O.16, H2O.17, H2O.21 ZN.14: 2 residues within 4Å: Chain B: D.100, D.104 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.100, B:D.104, H2O.16, H2O.17, H2O.18

4 x AWV: 3-(azepan-1-ylmethyl)-1~{H}-indole(Non-covalent)

AWV.6: 12 residues within 4Å: Chain A: R.53, Q.93, L.97, D.100, Q.169, K.209, T.210, Y.213, F.248, Q.249, D.252 Ligands: SO4.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.97, A:D.100, A:K.209 Hydrogen bonds: A:D.252 Water bridges: A:R.362 pi-Stacking: A:F.248 pi-Cation interactions: A:R.109 AWV.7: 6 residues within 4Å: Chain A: V.254, M.255, F.258, L.319, Q.320, F.323 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.254, A:F.258, A:F.258, A:F.323, A:F.323 AWV.15: 12 residues within 4Å: Chain B: R.53, Q.93, L.97, D.100, Q.169, K.209, T.210, Y.213, F.248, Q.249, D.252 Ligands: SO4.17 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.97, B:D.100, B:K.209 Hydrogen bonds: B:Y.213, B:D.252 Water bridges: B:R.362 pi-Stacking: B:F.248 pi-Cation interactions: B:R.109 AWV.16: 6 residues within 4Å: Chain B: V.254, M.255, F.258, L.319, Q.320, F.323 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.254, B:F.258, B:F.258, B:F.323, B:F.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petrick, J.K. et al., PanDDA analysis group deposition - FPPS screened against the DSI Fragment Library. To Be Published

Release Date

2020-04-29

Peptides

Farnesyl diphosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Farnesyl diphosphate synthase

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