Research workbench
Cryptococcus neoformans protein farnesyltransferase in complex with farnesyl-ddptasacniq product
Analyse Cryptococcus neoformans protein farnesyltransferase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q79
- Type
- protein
- Length
- 803 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyltransferase alpha subunit; Farnesyltransferase beta subunit; Isoprenylated product
- Ligands
- 3CX, FAR, ZN, SO4
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyltransferase alpha subunit | protein | 314 | 68% helix, 0% strand | — |
| B | Farnesyltransferase beta subunit | protein | 480 | 49% helix, 8% strand | — |
| P | Isoprenylated product | protein | 9 | 0% helix, 11% strand | — |
Ligands and binding sites
- 3CX · (2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid · ligand · 3 copies · chains B, A
- FAR · Farnesyl · ligand · chains A, B, P
- ZN · Zinc ion · metal · chains B, P
- SO4 · Sulfate ion · ion · chains 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 | 420 | 0.78 | 0.86 | 63 | FAR, SO4 |
| 2 | 409 | 0.76 | 0.85 | 43 | empty |
| 3 | 383 | 0.70 | 0.82 | 32 | empty |
| 4 | 454 | 0.62 | 0.76 | 43 | empty |
| 5 | 361 | 0.61 | 0.77 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3860 Ų buried · 65 hydrogen bonds · protein-protein
- B–P · 513 Ų buried · 8 hydrogen bonds · protein-protein
- A–P · 202 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (farnesylation).
Compared structures
- 3Q79 · Cryptococcus neoformans protein farnesyltransferase in complex with farnesyl-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 3Q79 · PDBe 3Q79
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