MolNFT v1 · #21318 · protein
Human protein farnesyltransferase complexed with L-778,123 and fpp
1S63 · Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type…: “Human protein farnesyltransferase complexed with L-778,123 and fpp”. X-ray diffraction, 5 ligands (FPP, 778, GLC), 11 pockets (best druggability 0.83). MolNFT v1 #21318…
- PDB
- 1S63
- Type
- protein
- Length
- 725 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, 778, GLC, FRU, ZN
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 4% 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 | 315 | 71% helix, 1% strand | P49354 |
| B | Protein farnesyltransferase beta subunit (EC 2.5.1.58) | protein | 410 | 50% helix, 7% strand | P49356 |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · chains A, B
- 778 · 4-[(5-{[4-(3-chlorophenyl)-3-oxopiperazin-1-yl]methyl}-1H-imidazol-1-yl)methyl]benzonitrile · ligand · chains A, B
- GLC · alpha-D-glucopyranose · sugar · chains A, B
- FRU · beta-D-fructofuranose · sugar · 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
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.83 | 0.90 | 77 | empty |
| 2 | 542 | 0.76 | 0.83 | 40 | FPP, 778 |
| 3 | 239 | 0.63 | 0.82 | 34 | empty |
| 4 | 233 | 0.52 | 0.76 | 28 | empty |
| 5 | 73 | 0.41 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3529 Ų buried · 79 hydrogen bonds · protein-protein
Compared structures
- 1S63 · Human protein farnesyltransferase complexed with L-778,123 and FPP · the same entry in another collection · chain B against B, 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 1S63 · PDBe 1S63 · UniProt P49354 · UniProt P49356
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