MolNFT v1 · #78660 · protein
Cryptococcus neoformans protein farnesyltransferase in complex with fpt-II and tipifarnib
3SFX · Cryptococcus neoformans protein farnesyltransferase alpha…: “Cryptococcus neoformans protein farnesyltransferase in complex with fpt-II and tipifarnib”. X-ray diffraction, 5 ligands (3FX, FII, JAN), 11 pockets (best druggability…
- PDB
- 3SFX
- Type
- protein
- Length
- 800 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cryptococcus neoformans protein farnesyltransferase alpha subunit; Cryptococcus…
- Ligands
- 3FX, FII, JAN, ZN, SO4
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cryptococcus neoformans protein farnesyltransferase alpha subunit | protein | 315 | 68% helix, 0% strand | — |
| B | Cryptococcus neoformans protein farnesyltransferase beta subunit | protein | 485 | 49% helix, 7% strand | — |
Ligands and binding sites
- 3FX · (2R)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid · ligand · 3 copies · chains B, A
- FII · [(3,7,11-trimethyl-dodeca-2,6,10-trienyloxycarbamoyl)-methyl]-phosphonic acid · ligand · chains A, B
- JAN · 6-[(S)-amino(4-chlorophenyl)(1-methyl-1H-imidazol-5-yl)methyl]-4-(3-chlorophenyl)-1-methylquinolin-2(1H)-one · ligand · chains B
- ZN · Zinc ion · metal · chains B
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.76 | 0.85 | 42 | empty |
| 2 | 834 | 0.74 | 0.78 | 66 | FII, JAN, SO4 |
| 3 | 548 | 0.67 | 0.78 | 60 | empty |
| 4 | 335 | 0.65 | 0.80 | 35 | empty |
| 5 | 59 | 0.53 | 0.87 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3779 Ų buried · 66 hydrogen bonds · protein-protein
Compared structures
- 3SFX · Cryptococcus neoformans protein farnesyltransferase in complex with FPT-II and tipifarnib · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3SFX · PDBe 3SFX
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