SMTL ID : 4llt.1

Crystal structure of a farnesyl diphosphate synthase from Roseobacter denitrificans OCh 114, target EFI-509393, with two IPP and calcium bound in active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

IPE.1: 11 residues within 4Å: Chain A: G.62, K.63, R.66, H.95, L.99, R.114, T.201, F.234, Q.235, D.238 Ligands: IPE.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.99, A:T.201 Hydrogen bonds: A:K.63 Water bridges: A:K.63, A:K.63, A:K.63, A:R.64, A:R.66, A:R.66, A:R.309 Salt bridges: A:K.63, A:K.63, A:R.66, A:H.95, A:H.95, A:R.114 IPE.2: 13 residues within 4Å: Chain A: S.98, L.99, D.102, D.108, R.113, M.171, Q.175, K.200, D.238, K.252 Ligands: IPE.1, CA.3, CA.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.99, A:D.102, A:K.200 Water bridges: A:D.108, A:D.110, A:R.113, A:Q.175, A:K.200, A:K.200, A:K.200, A:Q.235, A:K.252 Salt bridges: A:R.113, A:K.200, A:K.252, A:K.256 IPE.6: 11 residues within 4Å: Chain B: G.62, K.63, R.66, H.95, L.99, R.114, T.201, F.234, Q.235, D.238 Ligands: IPE.7 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.99, B:T.201, B:F.234 Hydrogen bonds: B:K.63 Water bridges: B:K.63, B:K.63, B:R.64, B:R.64, B:R.66, B:R.309, B:H.311 Salt bridges: B:K.63, B:K.63, B:R.66, B:H.95, B:H.95, B:R.114 IPE.7: 13 residues within 4Å: Chain B: S.98, L.99, D.102, D.108, R.113, M.171, Q.175, K.200, D.238, K.252 Ligands: IPE.6, CA.8, CA.9 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.99, B:D.102, B:K.200 Hydrogen bonds: B:D.108 Water bridges: B:R.113, B:Q.175, B:K.200, B:K.200, B:K.200, B:K.200, B:Q.235, B:K.252 Salt bridges: B:R.113, B:K.200, B:K.252

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: D.238 Ligands: IPE.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.238, H2O.3, H2O.3, H2O.4 CA.4: 3 residues within 4Å: Chain A: D.102, D.108 Ligands: IPE.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.102, A:D.108, H2O.3, H2O.6 CA.5: 3 residues within 4Å: Chain A: D.108, D.178, E.182 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.108, A:D.108, A:D.178, A:E.182, H2O.3 CA.8: 3 residues within 4Å: Chain B: D.102, D.108 Ligands: IPE.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.102, B:D.108, H2O.11, H2O.12 CA.9: 2 residues within 4Å: Chain B: D.238 Ligands: IPE.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.238, H2O.9, H2O.9, H2O.11 CA.10: 3 residues within 4Å: Chain B: D.108, D.178, K.200 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.108, B:D.178, H2O.11, H2O.12, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J. et al., Crystal structure of a farnesyl diphosphate synthase from Roseobacter denitrificans OCh 114, target EFI-509393, with two IPP and calcium bound in active site. To be Published

Release Date

2013-07-24

Peptides

Geranyltranstransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Geranyltranstransferase

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