MolNFT v1 · #11106 · protein
Crystal structure of rat protein farnesyltransferase complexed with the peptide substrate tkcvfm and an analog of farnesyl diphosphate
1JCS · Protein farnesyltransferase, alpha subunit: “Crystal structure of rat protein farnesyltransferase complexed with the peptide substrate tkcvfm and an…”. X-ray diffraction, 2 ligands (FII, ZN), 14 pockets (best druggability 0.78).…
- PDB
- 1JCS
- Type
- protein
- Length
- 736 residues
- Chains
- 3
- 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
- FII, ZN
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein farnesyltransferase, alpha subunit (EC 2.5.1.-) | protein | 323 | 70% helix, 1% strand | Q04631 |
| B | Protein farnesyltransferase, beta subunit (EC 2.5.1.-) | protein | 407 | 51% helix, 6% strand | Q02293 |
| C | Synthetic hexapeptide tkcvfm | protein | 6 | 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
- ACY · Acetic acid · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.78 | 0.85 | 55 | FII |
| 2 | 250 | 0.73 | 0.87 | 40 | empty |
| 3 | 270 | 0.67 | 0.83 | 45 | empty |
| 4 | 193 | 0.62 | 0.83 | 28 | empty |
| 5 | 145 | 0.45 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3513 Ų buried · 71 hydrogen bonds · protein-protein
- B–C · 445 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 207 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1JCS · Crystal structure of rat protein farnesyltransferase complexed with the peptide substrate… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.98
- Q04631 · AlphaFold monomer V2.0 prediction for protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERAS… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 1JCS · PDBe 1JCS · UniProt Q04631 · UniProt Q02293
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