SMTL ID : 5qq5.1

PanDDA analysis group deposition -- Crystal Structure of T. cruzi FPPS in complex with PKTTA024495b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: G.49, K.50, Y.51, F.52, R.53, Q.93 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.50, A:Y.51, A:F.52 Water bridges: A:G.49, A:R.53, A:R.53, A:R.53, A:E.90, A:R.110, A:R.110 Salt bridges: A:R.53 SO4.2: 4 residues within 4Å: Chain A: F.19, Q.23, H.143 Chain B: K.160 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Water bridges: B:K.160, B:K.160, B:K.160, A:H.143 Salt bridges: B:K.160, A:H.143 SO4.3: 7 residues within 4Å: Chain A: Y.96, L.97, D.100, T.165, Q.169, K.209, Y.213 No protein-ligand interaction detected (PLIP) SO4.8: 6 residues within 4Å: Chain B: G.49, K.50, Y.51, F.52, R.53, Q.93 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.50, B:Y.51, B:F.52 Water bridges: B:G.49, B:R.53, B:R.53, B:R.53, B:E.90, B:R.110, B:R.110 Salt bridges: B:R.53 SO4.9: 4 residues within 4Å: Chain A: K.160 Chain B: F.19, Q.23, H.143 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Water bridges: A:K.160, A:K.160, A:K.160, B:H.143 Salt bridges: A:K.160, B:H.143 SO4.10: 7 residues within 4Å: Chain B: Y.96, L.97, D.100, T.165, Q.169, K.209, Y.213 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.213

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

ACT.4: 3 residues within 4Å: Chain A: R.239, S.336, L.337 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.336 Salt bridges: A:R.239 ACT.11: 3 residues within 4Å: Chain B: R.239, S.336, L.337 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.336 Salt bridges: B:R.239

4 x ZN: ZINC ION(Non-covalent)

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.2, H2O.4, H2O.5 ZN.6: 3 residues within 4Å: Chain A: D.252, D.256, D.270 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.252, H2O.1, H2O.2, H2O.8, H2O.9 ZN.12: 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.15, H2O.17, H2O.18 ZN.13: 3 residues within 4Å: Chain B: D.252, D.256, D.270 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.252, H2O.14, H2O.14, H2O.20, H2O.22

2 x JJM: 1-methyl-N-(3-methylphenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine(Non-covalent)

JJM.7: 10 residues within 4Å: Chain A: P.199, Y.202, K.203, E.246, W.278, V.281, T.282, D.322, A.325, Y.326 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.199, A:K.203, A:E.246, A:V.281, A:Y.326, A:Y.326 Hydrogen bonds: A:W.278 pi-Stacking: A:W.278 JJM.14: 10 residues within 4Å: Chain B: P.199, Y.202, K.203, E.246, W.278, V.281, T.282, D.322, A.325, Y.326 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.199, B:K.203, B:E.246, B:V.281, B:Y.326, B:Y.326 Hydrogen bonds: B:W.278 pi-Stacking: B:W.278

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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