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Crystal structure of Aspergillus fumigatus protein farnesyltransferase complexed with the FII analog, FPT-II, and the KCVVM peptide
Analyse Crystal structure of Aspergillus fumigatus protein farnesyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L9P
- Type
- protein
- Length
- 792 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- Aspergillus fumigatus; SYNTHETIC CONSTRUCT
- Molecule
- CaaX farnesyltransferase alpha subunit Ram2; CaaX farnesyltransferase beta subunit Ram1…
- EC
- 2.5.1.-, 2.5.1.58
- UniProt
- Q4WP27, Q4WPS9
- Ligands
- FII, ZN, CL
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.45 · 3 distinct chains · 54% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CaaX farnesyltransferase alpha subunit Ram2 (EC 2.5.1.-) | protein | 335 | 65% helix, 0% strand | Q4WP27 |
| B | CaaX farnesyltransferase beta subunit Ram1 (EC 2.5.1.58) | protein | 452 | 46% helix, 6% strand | Q4WPS9 |
| C | LYS-CYS-VAL-VAL-MET (CAAX peptide) | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- FII · [(3,7,11-trimethyl-dodeca-2,6,10-trienyloxycarbamoyl)-methyl]-phosphonic acid · ligand · chains A, B, C
- ZN · Zinc ion · metal · chains B, C
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.80 | 0.83 | 79 | EDO, FII |
| 2 | 498 | 0.80 | 0.87 | 56 | EDO |
| 3 | 319 | 0.67 | 0.82 | 39 | empty |
| 4 | 262 | 0.62 | 0.80 | 33 | EDO |
| 5 | 103 | 0.54 | 0.84 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3683 Ų buried · 69 hydrogen bonds · protein-protein
- B–C · 330 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 191 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4L9P · Crystal structure of aspergillus fumigatus protein farnesyltransferase complexed with the… · 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
- Every structure of UniProt Q4WP27
- Every structure of UniProt Q4WPS9
- Elsewhere: RCSB PDB 4L9P · PDBe 4L9P · UniProt Q4WP27 · UniProt Q4WPS9
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