SMTL ID : 4l9p.1

Crystal structure of Aspergillus fumigatus protein farnesyltransferase complexed with the FII analog, FPT-II, and the KCVVM peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-1-1-mer

Ligands

1 x LYS- CYS- VAL- VAL- MET: LYS-CYS-VAL-VAL-MET (CAAX peptide)(Non-covalent)

LYS-CYS-VAL-VAL-MET.1: 13 residues within 4Å: Chain A: Y.88, Y.123, Q.124 Chain B: A.149, W.153, H.199, R.252, D.365, C.367, Y.432, H.433 Ligands: ZN.8, FII.15 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.123, B:Y.432 Hydrogen bonds: A:Q.124, B:R.252 Water bridges: A:Q.124, B:H.199

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: N.214, F.216 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: C.416, K.417, R.422 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: G.195, M.197 Ligand excluded by PLIP

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: P.143, P.144, R.145, E.146 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.145 EDO.4: 8 residues within 4Å: Chain A: T.57, L.60, R.61, M.64, H.87 Chain B: H.194, G.195 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.194, B:Q.196 EDO.5: 5 residues within 4Å: Chain A: Y.49, T.57, R.61 Chain B: D.148 Ligands: EDO.4 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.148, A:T.57, A:R.61, A:R.61 Water bridges: B:Q.196, A:T.57 EDO.6: 5 residues within 4Å: Chain A: E.257, Y.338, D.339 Chain B: P.80 Ligands: EDO.12 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.339 Water bridges: B:L.81, B:I.82, B:I.82 EDO.7: 3 residues within 4Å: Chain A: Q.130, S.134 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.130 EDO.11: 6 residues within 4Å: Chain B: Y.132, Y.140, M.154, W.157, D.430, S.431 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.132, B:S.431 Water bridges: B:Y.432 EDO.12: 3 residues within 4Å: Chain B: Q.94, Y.350 Ligands: EDO.6 5 PLIP interactions: 5 interactions with chain B Water bridges: B:Q.94, B:Q.94, B:A.351, B:A.351, B:N.361 EDO.13: 5 residues within 4Å: Chain B: Q.236, P.237, D.238, E.249 Ligands: EDO.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.236, B:D.238, B:D.238 Water bridges: B:D.238 EDO.14: 7 residues within 4Å: Chain A: H.127, Q.130 Chain B: T.242, G.247, E.249 Ligands: EDO.7, EDO.13 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:H.127, A:Q.130, B:E.249

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain B: D.365, C.367, Y.432, H.433 Ligands: LYS-CYS-VAL-VAL-MET.1 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.365, B:D.365, B:C.367, B:H.433

1 x FII: [(3,7,11-TRIMETHYL-DODECA-2,6,10-TRIENYLOXYCARBAMOYL)-METHYL]-PHOSPHONIC ACID(Non-covalent)

FII.15: 16 residues within 4Å: Chain A: Y.161, H.162 Chain B: W.153, R.252, Y.255, C.256, H.311, A.313, Y.314, C.317, R.359, K.362, Y.368, W.371, Y.432 Ligands: LYS-CYS-VAL-VAL-MET.1 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.153, B:R.252, B:Y.255, B:A.313, B:W.371, B:W.371, A:Y.161 Hydrogen bonds: B:R.359, B:K.362, B:K.362, B:Y.368 Water bridges: B:L.363, B:L.363

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mabanglo, M.F. et al., Crystal structures of the fungal pathogen Aspergillus fumigatus protein farnesyltransferase complexed with substrates and inhibitors reveal features for antifungal drug design. Protein Sci. (2014)

Release Date

2014-01-01

Peptides

CaaX farnesyltransferase alpha subunit Ram2: A
CaaX farnesyltransferase beta subunit Ram1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CaaX farnesyltransferase alpha subunit Ram2

CaaX farnesyltransferase beta subunit Ram1

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