Research workbench
Crystal structure of rat farnesyl transferase in complex with a potent biphenyl inhibitor
Analyse Crystal structure of rat farnesyl transferase in complex with a potent biphenyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NL4
- Type
- protein
- Length
- 713 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein farnesyltransferase alpha subunit; Protein farnesyltransferase beta subunit
- EC
- 2.5.1.-
- UniProt
- Q04631, Q02293
- Ligands
- HFP, FTL, ZN
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein farnesyltransferase alpha subunit (EC 2.5.1.-) | protein | 312 | 69% helix, 1% strand | Q04631 |
| B | Protein farnesyltransferase beta subunit (EC 2.5.1.-) | protein | 401 | 51% helix, 4% strand | Q02293 |
Ligands and binding sites
- HFP · Alpha-hydroxyfarnesylphosphonic acid · ligand · chains A, B
- FTL · 4-[(3-cyano-benzyl)-(3-methyl-3H-imidazol-4-ylmethyl)-amino]-2-naphthalen-1-yl-benzonitrile · ligand · chains A, B
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.76 | 0.79 | 71 | HFP, FTL |
| 2 | 243 | 0.75 | 0.89 | 35 | empty |
| 3 | 346 | 0.71 | 0.83 | 36 | empty |
| 4 | 382 | 0.65 | 0.79 | 46 | empty |
| 5 | 110 | 0.52 | 0.82 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3386 Ų buried · 72 hydrogen bonds · protein-protein
Compared structures
- 1NL4 · Crystal Structure of Rat Farnesyl Transferase in Complex With A Potent Biphenyl Inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q04631 · AlphaFold monomer V2.0 prediction for protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERAS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q02293 · AlphaFold monomer V2.0 prediction for protein farnesyltransferase subunit beta (Q02293) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q04631
- Every structure of UniProt Q02293
- Elsewhere: RCSB PDB 1NL4 · PDBe 1NL4 · UniProt Q04631 · UniProt Q02293
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