Research workbench
Crystal structure of rat protein farnesyltransferase complexed with the peptide substrate tkcvfm and an analog of farnesyl diphosphate
Analyse Crystal structure of rat protein farnesyltransferase complexed with the peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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