Research workbench
Co-crystal structure of human farnesyltransferase with farnesyldiphosphate and inhibitor compound 33A
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
- 1MZC
- 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, BNE, GLC, FRU, ZN
- Pockets
- 12 · best druggability 0.80
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 | 70% helix, 1% strand | P49354 |
| B | Protein farnesyltransferase beta subunit (EC 2.5.1.-) | protein | 407 | 50% helix, 7% strand | P49356 |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · chains A, B
- BNE · 2-[3-(3-ethyl-1-methyl-2-oxo-azepan-3-yl)-phenoxy]-4-[1-amino-1-(1-methyl-1H-imidizol-5-yl)-ethyl]-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
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.80 | 0.91 | 48 | empty |
| 2 | 956 | 0.77 | 0.79 | 62 | FPP, BNE |
| 3 | 216 | 0.63 | 0.82 | 28 | empty |
| 4 | 253 | 0.63 | 0.81 | 36 | empty |
| 5 | 209 | 0.51 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 3564 Ų buried · 72 hydrogen bonds · protein-protein
Compared structures
- 1MZC · Co-Crystal Structure Of Human Farnesyltransferase With Farnesyldiphosphate and Inhibitor… · 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 1MZC · PDBe 1MZC · UniProt P49354 · UniProt P49356
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