SMTL ID : 6t7n.1

Trypanosoma cruzi farnesyl diphosphate synthase in complex with IPP and Mn

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: D.98, D.102, S.104, R.107 Ligands: MN.3, IPE.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.2, H2O.4 MN.2: 5 residues within 4Å: Chain A: Q.247, D.250, D.254, K.264 Ligands: IPE.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.250, H2O.1, H2O.1, H2O.5 MN.3: 7 residues within 4Å: Chain A: D.98, D.102, Q.167, D.170, K.273 Ligands: MN.1, IPE.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.98, A:D.102, H2O.1, H2O.1, H2O.1 MN.6: 6 residues within 4Å: Chain B: D.98, D.102, S.104, R.107 Ligands: MN.8, IPE.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.8, H2O.10 MN.7: 5 residues within 4Å: Chain B: Q.247, D.250, D.254, K.264 Ligands: IPE.9 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.250, H2O.7, H2O.7, H2O.12 MN.8: 7 residues within 4Å: Chain B: D.98, D.102, Q.167, D.170, K.273 Ligands: MN.6, IPE.9 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.98, B:D.102, H2O.7, H2O.7, H2O.8

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

IPE.4: 17 residues within 4Å: Chain A: Y.94, L.95, D.98, D.102, R.107, T.163, Q.167, K.207, T.208, Y.211, Q.247, D.250, K.264 Ligands: MN.1, MN.2, MN.3, IPE.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:D.98, A:T.163, A:Q.167, A:K.207 Hydrogen bonds: A:Q.247 Water bridges: A:S.104, A:R.107, A:Q.167, A:K.207, A:K.207, A:K.207, A:D.254, A:D.254, A:D.254, A:K.273 Salt bridges: A:R.107, A:K.207, A:K.264 IPE.5: 16 residues within 4Å: Chain A: G.47, K.48, Y.49, R.51, Q.91, L.95, R.107, R.108, T.208, Y.211, F.246, Q.247, D.250, K.264, R.360 Ligands: IPE.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.95, A:D.250 Hydrogen bonds: A:K.48, A:R.51, A:Q.91, A:R.360 Water bridges: A:K.48, A:K.48, A:Y.49, A:Y.49, A:Y.49, A:K.264 Salt bridges: A:K.48, A:K.48, A:R.51, A:R.108 IPE.9: 17 residues within 4Å: Chain B: Y.94, L.95, D.98, D.102, R.107, T.163, Q.167, K.207, T.208, Y.211, Q.247, D.250, K.264 Ligands: MN.6, MN.7, MN.8, IPE.10 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:D.98, B:T.163, B:Q.167, B:K.207 Hydrogen bonds: B:Q.247 Water bridges: B:S.104, B:R.107, B:Q.167, B:K.207, B:K.207, B:K.207, B:K.273 Salt bridges: B:R.107, B:K.207, B:K.264 IPE.10: 16 residues within 4Å: Chain B: G.47, K.48, Y.49, R.51, Q.91, L.95, R.107, R.108, T.208, Y.211, F.246, Q.247, D.250, K.264, R.360 Ligands: IPE.9 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.95, B:D.250 Hydrogen bonds: B:K.48, B:R.51, B:Q.91, B:R.360 Water bridges: B:K.48, B:K.48, B:Y.49, B:Y.49, B:Y.49, B:K.264 Salt bridges: B:K.48, B:K.48, B:R.51, B:R.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Magari, F. et al., Trypanosoma cruzi farnesyl diphosphate synthase in complex with IPP and Mn. To Be Published

Release Date

2020-11-18

Peptides

Farnesyl diphosphate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAAA

B
AAAA

Farnesyl diphosphate synthase

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