Research workbench
Cryptococcus neoformans protein farnesyltransferase in complex with fspp and ddptasacniq peptide
Analyse Cryptococcus neoformans protein farnesyltransferase in complex with fspp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q78
- Type
- protein
- Length
- 799 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyltransferase alpha subunit; Farnesyltransferase beta subunit; Peptide substrate
- Ligands
- 3CX, FPS, ZN
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyltransferase alpha subunit | protein | 312 | 67% helix, 0% strand | — |
| B | Farnesyltransferase beta subunit | protein | 478 | 50% helix, 7% strand | — |
| D | Peptide substrate | protein | 9 | 0% helix, 11% strand | — |
Ligands and binding sites
- 3CX · (2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid · ligand · 2 copies · chains B
- FPS · S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen thiodiphosphate · ligand · chains A, B, D
- ZN · Zinc ion · metal · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.77 | 0.88 | 43 | empty |
| 2 | 426 | 0.76 | 0.85 | 55 | FPS |
| 3 | 367 | 0.73 | 0.84 | 40 | empty |
| 4 | 477 | 0.64 | 0.77 | 44 | empty |
| 5 | 342 | 0.62 | 0.78 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3870 Ų buried · 73 hydrogen bonds · protein-protein
- B–D · 541 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 199 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3Q78 · Cryptococcus neoformans protein farnesyltransferase in complex with FSPP and DDPTASACNIQ… · 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 3Q78 · PDBe 3Q78
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