Research workbench
Structure of rat farnesyl protein transferase complexed with a cvim peptide and alpha-hydroxyfarnesylphosphonic acid.
Analyse Structure of rat farnesyl protein transferase complexed with a cvim peptide and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QBQ
- Type
- protein
- Length
- 717 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fpt alpha-subunit; Fpt beta-subunit; Acetyl-cys-val-ile-selenomet-cooh peptide
- EC
- 2.5.1.-
- UniProt
- Q04631, Q02293
- Ligands
- ACE, HFP, ZN
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fpt alpha-subunit (EC 2.5.1.-) | protein | 312 | 68% helix, 1% strand | Q04631 |
| B | Fpt beta-subunit (EC 2.5.1.-) | protein | 401 | 50% helix, 4% strand | Q02293 |
| P | Acetyl-cys-val-ile-selenomet-cooh peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains P
- HFP · Alpha-hydroxyfarnesylphosphonic acid · ligand · chains A, B, P
- ZN · Zinc ion · metal · chains B, P
- ACT · Acetate ion · additive · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.76 | 0.96 | 20 | empty |
| 2 | 182 | 0.74 | 0.91 | 31 | empty |
| 3 | 420 | 0.73 | 0.83 | 49 | ACE, HFP |
| 4 | 211 | 0.62 | 0.82 | 27 | empty |
| 5 | 243 | 0.56 | 0.78 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3455 Ų buried · 75 hydrogen bonds · protein-protein
- B–P · 309 Ų buried · 1 hydrogen bond · protein-protein
- A–P · 162 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, engineered).
Compared structures
- 1QBQ · Structure of rat farnesyl protein transferase complexed with a cvim peptide and… · 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 1QBQ · PDBe 1QBQ · UniProt Q04631 · UniProt Q02293
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