Research workbench
Zinc-depleted ftase complexed with K-RAS4B peptide substrate and fpp analog.
Analyse Zinc-depleted ftase complexed with K-RAS4B peptide substrate and fpp analog. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D8E
- Type
- protein
- Length
- 736 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyltranserase (alpha subunit); Farnesyltranserase (beta subunit); K-RAS4B peptide…
- EC
- 2.5.1.21
- UniProt
- Q04631, Q02293, P01116
- Ligands
- FII
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyltranserase (alpha subunit) (EC 2.5.1.21) | protein | 323 | 68% helix, 1% strand | Q04631 |
| B | Farnesyltranserase (beta subunit) (EC 2.5.1.21) | protein | 407 | 51% helix, 6% strand | Q02293 |
| P | K-RAS4B peptide substrate | protein | 6 | 0% helix, 0% strand | P01116 |
Ligands and binding sites
- FII · [(3,7,11-trimethyl-dodeca-2,6,10-trienyloxycarbamoyl)-methyl]-phosphonic acid · ligand · chains A, B, P
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.82 | 0.85 | 99 | FII |
| 2 | 119 | 0.78 | 0.96 | 26 | empty |
| 3 | 198 | 0.60 | 0.82 | 28 | empty |
| 4 | 119 | 0.48 | 0.80 | 23 | empty |
| 5 | 144 | 0.48 | 0.78 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3553 Ų buried · 81 hydrogen bonds · protein-protein
- B–P · 433 Ų buried · 1 hydrogen bond · protein-protein
- A–P · 191 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1D8E · Zinc-depleted FTase complexed with K-RAS4B peptide substrate and FPP analog. · 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 P01116
- Elsewhere: RCSB PDB 1D8E · PDBe 1D8E · UniProt Q04631 · UniProt Q02293 · UniProt P01116
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