MolNFT v1 · #13050 · protein
Protein farnesyltransferase complexed with a farnesylated K-RAS4B peptide product
1KZP · Protein farnesyltransferase alpha subunit: “Protein farnesyltransferase complexed with a farnesylated K-RAS4B peptide product”. X-ray diffraction, 2 ligands (FAR, ZN), 13 pockets (best druggability 0.76). MolNFT v1 #13050 on…
- PDB
- 1KZP
- Type
- protein
- Length
- 735 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
- 2.5.1.21
- UniProt
- Q04631, Q02293, P01118
- Ligands
- FAR, ZN
- Pockets
- 13 · best druggability 0.76
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 2.5.1.21) | protein | 323 | 67% helix, 1% strand | Q04631 |
| B | Protein farnesyltransferase beta subunit (EC 2.5.1.21) | protein | 407 | 52% helix, 6% strand | Q02293 |
| C | Farnesylated K-RAS4B peptide product | protein | 5 | 0% helix, 0% strand | P01118 |
Ligands and binding sites
- FAR · Farnesyl · 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
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.76 | 0.96 | 25 | empty |
| 2 | 454 | 0.75 | 0.84 | 50 | FAR |
| 3 | 265 | 0.73 | 0.87 | 41 | empty |
| 4 | 182 | 0.61 | 0.82 | 26 | empty |
| 5 | 148 | 0.54 | 0.81 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3505 Ų buried · 74 hydrogen bonds · protein-protein
- B–C · 329 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 160 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 lipid (farnesylation).
Compared structures
- 1KZP · Protein farnesyltransferase complexed with a farnesylated K-RAS4B peptide product · 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
- Every structure of UniProt P01118
- Elsewhere: RCSB PDB 1KZP · PDBe 1KZP · UniProt Q04631 · UniProt Q02293 · UniProt P01118
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