Research workbench
Cryptococcus neoformans protein farnesyltransferase in complex with fpt-II and ethylenediamine inhibitor 2
Analyse Cryptococcus neoformans protein farnesyltransferase in complex with fpt-II and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SFY
- Type
- protein
- Length
- 797 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, 3FY, FII, ZN, SO4
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 56% 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 | 482 | 48% helix, 7% strand | — |
Ligands and binding sites
- 3FX · (2R)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid · ligand · 3 copies · chains B, A
- 3FY · N-(2-{(4-bromophenyl)[(1-methyl-1H-imidazol-5-yl)methyl]amino}ethyl)-1-methyl-N-(2-methylbenzyl)-1H-imidazole-4-sulfonamide · ligand · chains A, B
- FII · [(3,7,11-trimethyl-dodeca-2,6,10-trienyloxycarbamoyl)-methyl]-phosphonic acid · ligand · chains A, 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
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.75 | 0.85 | 41 | empty |
| 2 | 898 | 0.74 | 0.78 | 74 | 3FY, FII, SO4 |
| 3 | 356 | 0.70 | 0.82 | 30 | empty |
| 4 | 497 | 0.64 | 0.76 | 48 | empty |
| 5 | 53 | 0.52 | 0.88 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3780 Ų buried · 70 hydrogen bonds · protein-protein
Compared structures
- 3SFY · Cryptococcus neoformans protein farnesyltransferase in complex with FPT-II and… · 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 3SFY · PDBe 3SFY
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.