Research workbench
Structure of fpt bound to datfp-dh-gpp
Analyse Structure of fpt bound to datfp-dh-gpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KSL
- Type
- protein
- Length
- 718 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyltransferase, caax box, alpha; Protein farnesyltransferase subunit beta
- EC
- 2.5.1.58
- UniProt
- Q5RKJ4, Q02293
- Ligands
- SZH, MG, ZN
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyltransferase, caax box, alpha (EC 2.5.1.58) | protein | 315 | 68% helix, 1% strand | Q5RKJ4 |
| B | Protein farnesyltransferase subunit beta (EC 2.5.1.58) | protein | 403 | 52% helix, 7% strand | Q02293 |
Ligands and binding sites
- SZH · (2S,6E)-8-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}-2,6-dimethyloct-6-en-1-yl (2S)-3,3,3-trifluoro-2-hydrazinopropanoate · ligand · chains A, B
- MG · Magnesium ion · metal · 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 | 1020 | 0.78 | 0.79 | 69 | MG, SZH |
| 2 | 79 | 0.74 | 0.97 | 25 | empty |
| 3 | 191 | 0.74 | 0.90 | 34 | empty |
| 4 | 302 | 0.58 | 0.77 | 39 | empty |
| 5 | 65 | 0.48 | 0.84 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3514 Ų buried · 77 hydrogen bonds · protein-protein
Compared structures
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 Q5RKJ4
- Every structure of UniProt Q02293
- Elsewhere: RCSB PDB 3KSL · PDBe 3KSL · UniProt Q5RKJ4 · UniProt Q02293
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