Research workbench
Co-crystal structure of human farnesyltransferase with farnesyldiphosphate and inhibitor compound 49
Analyse Co-crystal structure of human farnesyltransferase with farnesyldiphosphate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LD8
- Type
- protein
- Length
- 720 residues
- Chains
- 2
- 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.-
- UniProt
- P49354, P49356
- Ligands
- FPP, U49, GLC, FRU, ZN
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein farnesyltransferase alpha subunit (EC 2.5.1.-) | protein | 313 | 71% helix, 1% strand | P49354 |
| B | Protein farnesyltransferase beta subunit (EC 2.5.1.-) | protein | 407 | 51% helix, 7% strand | P49356 |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · chains A, B
- U49 · (20S)-19,20,21,22-tetrahydro-19-oxo-5H-18,20-ethano-12,14-etheno-6,10-metheno-18H-benz[d]imidazo[4,3-k][1,6,9,12]oxatri aza-cyclooctadecosine-9-carbonitrile · 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
- ACY · Acetic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.76 | 0.79 | 67 | ACY, FPP, U49 |
| 2 | 228 | 0.74 | 0.89 | 38 | empty |
| 3 | 300 | 0.72 | 0.86 | 48 | empty |
| 4 | 223 | 0.61 | 0.81 | 33 | empty |
| 5 | 169 | 0.50 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 3563 Ų buried · 72 hydrogen bonds · protein-protein
Compared structures
- 1LD8 · Co-crystal structure of Human Farnesyltransferase with farnesyldiphosphate and inhibitor… · 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 1LD8 · PDBe 1LD8 · UniProt P49354 · UniProt P49356
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