SMTL ID : 6w7i.1

LmFPPS mutant T164W in complex with 476A, IPP & Ca

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: D.250 Ligands: 476.6, PEG.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.250, H2O.1, H2O.2, H2O.4 CA.2: 5 residues within 4Å: Chain A: D.98, D.102 Ligands: CA.3, 476.6, PEG.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.2, H2O.7 CA.3: 4 residues within 4Å: Chain A: D.98, D.102 Ligands: CA.2, 476.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.1, H2O.2, H2O.7 CA.8: 2 residues within 4Å: Chain B: D.250 Ligands: 476.12 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.250, H2O.10, H2O.12, H2O.13 CA.9: 4 residues within 4Å: Chain B: D.98, D.102 Ligands: CA.10, 476.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.11, H2O.16 CA.10: 5 residues within 4Å: Chain B: D.98, D.102, D.170 Ligands: CA.9, 476.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.10, H2O.13, H2O.15

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

ACT.4: 9 residues within 4Å: Chain A: D.254, C.255, G.266, T.267, D.268, I.269, E.270, V.305, K.309 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.269 Salt bridges: A:K.309

2 x IPR: ISOPENTYL PYROPHOSPHATE(Non-covalent)

IPR.5: 12 residues within 4Å: Chain A: G.47, K.48, R.51, Q.91, L.95, R.108, T.208, Y.211, F.246, Q.247, D.250 Ligands: 476.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.95, A:T.208, A:D.250 Hydrogen bonds: A:K.48, A:R.51 Water bridges: A:K.48, A:Y.49, A:K.264, A:K.264 Salt bridges: A:K.48, A:K.48, A:R.51, A:R.108 IPR.11: 12 residues within 4Å: Chain B: G.47, K.48, R.51, Q.91, L.95, R.108, T.208, Y.211, F.246, Q.247, D.250 Ligands: 476.12 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.95, B:T.208 Hydrogen bonds: B:K.48, B:R.51, B:Q.91 Water bridges: B:K.48, B:Y.49, B:K.264, B:K.264 Salt bridges: B:K.48, B:K.48, B:R.51, B:R.108, B:K.264

2 x 476: 3-butyl-1-(2,2-diphosphonoethyl)pyridinium(Non-covalent)

476.6: 19 residues within 4Å: Chain A: F.94, D.98, M.101, D.102, R.107, T.163, W.164, Q.167, K.207, T.208, Y.211, Q.247, D.250, K.264 Ligands: CA.1, CA.2, CA.3, IPR.5, PEG.7 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.94, A:F.94, A:D.98, A:T.163, A:W.164, A:W.164, A:Q.167, A:K.207, A:K.207, A:Y.211 Hydrogen bonds: A:R.107, A:R.107, A:K.207, A:Q.247, A:K.264 Water bridges: A:D.98, A:S.104, A:Q.167, A:K.264 476.12: 18 residues within 4Å: Chain B: F.94, D.98, M.101, D.102, R.107, T.163, W.164, Q.167, K.207, T.208, Y.211, Q.247, D.250, K.264 Ligands: CA.8, CA.9, CA.10, IPR.11 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.94, B:F.94, B:T.163, B:Q.167, B:K.207, B:Y.211 Hydrogen bonds: B:R.107, B:R.107, B:K.207, B:Q.247, B:K.264 Water bridges: B:D.98, B:S.104, B:S.104, B:Q.167, B:K.264

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

PEG.7: 12 residues within 4Å: Chain A: D.99, S.104, T.106, R.107, D.254, L.262, K.264, I.265, G.266 Ligands: CA.1, CA.2, 476.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.106, A:D.254 Water bridges: A:S.104, A:R.107, A:I.265, A:I.265, A:G.266, A:T.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maheshwari, S. et al., Identifying Structural Determinants of Product Specificity in Leishmania major Farnesyl Diphosphate Synthase. Biochemistry (2020)

Release Date

2020-10-07

Peptides

Farnesyl pyrophosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Farnesyl pyrophosphate synthase