SMTL ID : 4q9m.1

Crystal structure of UPPs in complex with FPP and an allosteric inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

2 x 2ZW: 3-(2-chlorophenyl)-5-methyl-N-[4-(propan-2-yl)phenyl]-1,2-oxazole-4-carboxamide(Non-covalent)

2ZW.1: 22 residues within 4Å: Chain A: M.43, L.46, Q.47, A.65, F.66, I.81, M.82, L.84, P.85, F.88, Y.89, Y.92, V.93, L.96, I.103, T.116, A.119, L.120, A.123, F.137, L.139 Ligands: FPP.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.81, A:P.85, A:P.85, A:Y.89, A:Y.92, A:V.93, A:T.116, A:L.120, A:A.123, A:F.137, A:F.137, A:F.137, A:L.139 Halogen bonds: A:F.88 2ZW.12: 22 residues within 4Å: Chain B: M.43, L.46, Q.47, A.65, F.66, I.81, M.82, L.84, P.85, F.88, Y.89, Y.92, V.93, L.96, I.103, T.116, A.119, L.120, A.123, F.137, L.139 Ligands: FPP.13 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.46, B:I.81, B:P.85, B:P.85, B:Y.89, B:V.93, B:L.120, B:A.123, B:F.137, B:L.139 Halogen bonds: B:F.88

2 x FPP: FARNESYL DIPHOSPHATE(Non-covalent)

FPP.2: 17 residues within 4Å: Chain A: M.21, D.22, G.23, N.24, G.25, R.26, R.35, H.39, G.42, M.43, L.46, A.65, R.73, I.81, F.137 Ligands: 2ZW.1, CD.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:H.39, A:A.65, A:I.81, A:F.137 Hydrogen bonds: A:G.23, A:N.24, A:G.25, A:R.26, A:R.35 Water bridges: A:R.26, A:R.73 Salt bridges: A:R.26, A:R.35, A:H.39, A:R.73 FPP.13: 18 residues within 4Å: Chain B: M.21, D.22, G.23, N.24, G.25, R.26, R.35, H.39, G.42, M.43, L.46, A.65, N.70, R.73, I.81, F.137 Ligands: 2ZW.12, CD.14 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:H.39, B:A.65, B:I.81, B:F.137 Hydrogen bonds: B:G.23, B:N.24, B:G.25, B:R.26, B:R.35 Water bridges: B:R.26, B:R.73 Salt bridges: B:R.26, B:R.35, B:R.73

15 x CD: CADMIUM ION(Non-covalent)

CD.3: 2 residues within 4Å: Chain A: D.22 Ligands: FPP.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.22, H2O.1, H2O.1, H2O.2 CD.4: 2 residues within 4Å: Chain A: E.108, D.110 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.108, A:D.110, A:D.110, H2O.1 CD.5: 1 residues within 4Å: Chain A: E.170 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.170, A:E.170, H2O.1, H2O.1, H2O.8 CD.6: 1 residues within 4Å: Chain A: D.185 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.185, H2O.2, H2O.3, H2O.3 CD.7: 1 residues within 4Å: Chain A: D.90 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.90, H2O.8, H2O.8, H2O.8 CD.8: 2 residues within 4Å: Chain A: E.44 Ligands: CD.10 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.44, A:E.44 CD.9: 2 residues within 4Å: Chain A: E.198, R.200 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.198, H2O.6 CD.10: 3 residues within 4Å: Chain A: K.51, E.95 Ligands: CD.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.95 CD.11: 1 residues within 4Å: Chain A: D.157 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.157, A:D.157, H2O.6, H2O.7 CD.14: 2 residues within 4Å: Chain B: D.22 Ligands: FPP.13 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.22, H2O.9, H2O.10, H2O.10 CD.15: 1 residues within 4Å: Chain B: D.185 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.185, H2O.9, H2O.9, H2O.16 CD.16: 2 residues within 4Å: Chain B: E.69, S.202 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.69, B:E.69, H2O.9, H2O.9, H2O.12 CD.17: 1 residues within 4Å: Chain B: E.170 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.170, B:E.170, H2O.1, H2O.15 CD.18: 2 residues within 4Å: Chain A: H.240 Chain B: E.198 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.198, B:E.198, A:H.240, H2O.11, H2O.13 CD.19: 1 residues within 4Å: Chain B: D.157 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.157, B:D.157, H2O.13, H2O.13, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Danley, D.E. et al., Discovery and structural characterization of an allosteric inhibitor of bacterial cis-prenyltransferase. Protein Sci. (2015)

Release Date

2014-10-15

Peptides

Isoprenyl transferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoprenyl transferase

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