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Crystal structure of human protein farnesyltransferase complexed with farnesyl diphosphate and hydantoin derivative
Analyse Crystal structure of human protein farnesyltransferase complexed with farnesyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F0Y
- Type
- protein
- Length
- 709 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type I alpha subunit; Protein…
- EC
- 2.5.1.58, 2.5.1.59
- UniProt
- P49354, P49356
- Ligands
- FPP, 3MN, ZN
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type I alpha subunit (EC 2.5.1.58, 2.5.1.59) | protein | 314 | 70% helix, 1% strand | P49354 |
| B | Protein farnesyltransferase beta subunit (EC 2.5.1.58) | protein | 395 | 51% helix, 4% strand | P49356 |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · chains A, B
- 3MN · 3-({3-[3-(1H-imidazol-1-yl)propyl]-5-methyl-5-(1-naphthyl)-2,4-dioxoimidazolidin-1-yl}methyl)benzonitrile · ligand · chains A, B
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.81 | 0.89 | 65 | empty |
| 2 | 701 | 0.76 | 0.81 | 49 | FPP, 3MN |
| 3 | 55 | 0.60 | 0.92 | 12 | empty |
| 4 | 263 | 0.58 | 0.78 | 28 | empty |
| 5 | 88 | 0.50 | 0.83 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3578 Ų buried · 67 hydrogen bonds · protein-protein
Compared structures
- 2F0Y · Crystal Structure Of Human Protein Farnesyltransferase Complexed With Farnesyl… · the same entry in another collection · chain A against A, TM-score 1.00
- P49356 · AlphaFold monomer V2.0 prediction for protein farnesyltransferase subunit beta (P49356) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P49354 · AlphaFold monomer V2.0 prediction for protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERAS… · a predicted model of the same protein · chain A 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 P49354
- Every structure of UniProt P49356
- Elsewhere: RCSB PDB 2F0Y · PDBe 2F0Y · UniProt P49354 · UniProt P49356
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