Research workbench
Protein farnesyltransferase complexed with fpp and ethylenediamine-scaffold inhibitor 10
Analyse Protein farnesyltransferase complexed with fpp and ethylenediamine-scaffold… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E34
- Type
- protein
- Length
- 730 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type-1 subunit alpha; Protein…
- EC
- 2.5.1.58, 2.5.1.59
- UniProt
- Q04631, Q02293
- Ligands
- FPP, ED1, ZN
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type-1 subunit alpha (EC 2.5.1.58, 2.5.1.59) | protein | 323 | 68% helix, 1% strand | Q04631 |
| B | Protein farnesyltransferase subunit beta (EC 2.5.1.58) | protein | 407 | 51% helix, 7% strand | Q02293 |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · chains A, B
- ED1 · 3-{2'-[{[1-(tert-butoxycarbonyl)piperidin-4-yl]methyl}(2-{(4-cyanophenyl)[(1-methyl-1H-imidazol-5-yl)methyl]amino}ethyl)sulfamoyl]biphenyl-3-yl}propanoic acid · 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
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 358 | 0.81 | 0.90 | 58 | empty |
| 2 | 832 | 0.75 | 0.79 | 54 | FPP, ED1 |
| 3 | 184 | 0.61 | 0.82 | 26 | empty |
| 4 | 155 | 0.47 | 0.76 | 21 | empty |
| 5 | 94 | 0.45 | 0.80 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 3526 Ų buried · 77 hydrogen bonds · protein-protein
Compared structures
- 3E34 · Protein farnesyltransferase complexed with FPP and ethylenediamine-scaffold inhibitor 10 · 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 3E34 · PDBe 3E34 · UniProt Q04631 · UniProt Q02293
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