MolNFT v1 · #11105 · protein
Crystal structure of rat protein farnesyltransferase complexed with the non-substrate tetrapeptide inhibitor cvfm and farnesyl diphosphate substrate
1JCR · Protein farnesyltransferase, alpha subunit: “Crystal structure of rat protein farnesyltransferase complexed with the non-substrate tetrapeptide inhibitor…”. X-ray diffraction, 2 ligands (FPP, ZN), 14 pockets (best druggability…
- PDB
- 1JCR
- Type
- protein
- Length
- 734 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
- FPP, ZN
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein farnesyltransferase, alpha subunit (EC 2.5.1.-) | protein | 323 | 67% helix, 1% strand | Q04631 |
| B | Protein farnesyltransferase, beta subunit (EC 2.5.1.-) | protein | 407 | 51% helix, 6% strand | Q02293 |
| C | Synthetic tetrapeptide cvfm | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · chains A, B, C
- ZN · Zinc ion · metal · chains B, C
- ACY · Acetic acid · additive · 2 copies · chains A, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.75 | 0.97 | 23 | empty |
| 2 | 328 | 0.74 | 0.86 | 50 | FPP |
| 3 | 251 | 0.74 | 0.88 | 41 | empty |
| 4 | 186 | 0.60 | 0.82 | 26 | ACY |
| 5 | 361 | 0.59 | 0.76 | 54 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3506 Ų buried · 72 hydrogen bonds · protein-protein
- B–C · 334 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 189 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1JCR · Crystal structure of rat protein farnesyltransferase complexed with the non-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 1JCR · PDBe 1JCR · UniProt Q04631 · UniProt Q02293
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