SMTL ID : 8t70.1

Cryptococcus neoformans protein farnesyltransferase in complex with FPTII and TKCMIIM peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MET- ILE- ILE- MET: MET-ILE-ILE-MET(Non-covalent)

MET-ILE-ILE-MET.1: 18 residues within 4Å: Chain A: Y.88, Y.123, Q.124 Chain B: F.81, L.84, A.86, S.87, W.90, W.94, H.139, L.141, P.142, R.197, D.407, Q.408, Y.409 Ligands: FII.14, BT6.15 12 PLIP interactions: 2 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:Q.124, B:R.197 Water bridges: A:Q.124, B:S.87, B:H.139, B:D.407 Hydrophobic interactions: B:W.90, B:W.94, B:W.94, B:L.141, B:Y.409, B:Y.409

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

EDO.2: 5 residues within 4Å: Chain A: L.109, N.113, R.129, S.143, E.144 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: H.240, V.242, V.301, P.302, L.303 Ligands: EDO.4 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: V.242, P.302, D.333, R.336 Chain B: E.307 Ligands: EDO.3, EDO.22 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: Y.88, W.91, Q.124, H.127, H.128 Chain B: C.189, E.193 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: R.195, V.196, D.197, G.198, L.237, I.238 Chain B: R.22, P.23 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: I.178, W.183, G.216 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: R.211, E.218, S.223, L.224, E.227, F.255 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: R.26, W.29, R.72, E.75, I.79 Ligand excluded by PLIP EDO.16: 9 residues within 4Å: Chain B: D.210, I.211, I.212, W.457, A.466, R.467, I.470, Y.516 Ligands: EDO.20 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: H.127, L.130 Chain B: R.181, E.193, V.194 Ligands: EDO.23 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain B: A.105, K.111, R.507 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: G.103, V.104, A.105 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: D.210, I.212, A.447, V.448, R.463, R.467 Ligands: EDO.16 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain B: M.425, W.477, T.496, T.497, T.498, L.504, G.505 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain A: R.336 Chain B: L.303, Q.304, Q.305, G.306, E.307, R.315 Ligands: EDO.4 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: L.130, A.163, W.167 Chain B: M.262 Ligands: EDO.17 Ligand excluded by PLIP EDO.24: 9 residues within 4Å: Chain A: Q.37, Y.49, M.57, R.61 Chain B: D.85, G.131, P.132, S.135, Q.136 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain B: A.441, K.443, G.444, L.445, R.463, Q.464, R.467 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: A.166, A.167, R.169, Q.170, P.446 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: Q.390, R.405, P.406 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: R.178, C.179, K.180, R.181, V.187 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: P.124, K.125, Q.170, S.171, E.174 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: I.292, D.293, A.294, N.295, E.344 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain B: D.323, C.325, Y.409, H.410 Ligands: BT6.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.323, B:D.323, B:C.325, B:H.410

3 x 3FX: (2R)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid(Non-covalent)

3FX.11: 4 residues within 4Å: Chain B: Y.58, G.489, K.490, D.491 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.490, B:D.491, B:D.491, B:D.491 Water bridges: B:Y.58, B:N.492 3FX.12: 4 residues within 4Å: Chain B: R.62, K.63, Q.64, E.65 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.62, B:Q.64, B:E.65 Water bridges: B:K.63, B:K.63 3FX.13: 10 residues within 4Å: Chain A: A.64, T.89 Chain B: S.123, P.124, K.125, A.133, N.134, S.135, Q.136, I.137 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.137, A:A.64, A:T.89 Hydrogen bonds: B:K.125

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

FII.14: 17 residues within 4Å: Chain A: Y.123, Y.159 Chain B: L.141, R.197, Y.200, C.201, H.266, G.268, Y.269, C.272, R.317, K.320, Y.326, W.329, Y.409 Ligands: MET-ILE-ILE-MET.1, BT6.15 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.141, B:R.197, B:Y.200, B:Y.269, B:W.329, B:W.329, A:Y.159 Hydrogen bonds: B:R.317, B:K.320, B:Y.326, B:Y.326 Water bridges: B:R.317, B:K.320, A:Y.159

1 x BT6: benzenethiol(Non-covalent)

BT6.15: 9 residues within 4Å: Chain B: H.266, D.323, C.325, Y.326, Y.409, H.410 Ligands: MET-ILE-ILE-MET.1, ZN.10, FII.14 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Cryptococcus neoformans protein farnesyltransferase in complex with FPTII and TKCMIIM peptide. To Be Published

Release Date

2023-08-09

Peptides

Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha: A
Protein farnesyltransferase subunit beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha

Protein farnesyltransferase subunit beta

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