MolNFT v1 · #61585 · protein
Protein farnesyltransferase complexed with fpp and caged tkcvim substrate
3DPY · Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type…: “Protein farnesyltransferase complexed with fpp and caged tkcvim substrate”. X-ray diffraction, 2 ligands (FPP, ZN), 12 pockets (best druggability 0.75). MolNFT v1 #61585…
- PDB
- 3DPY
- Type
- protein
- Length
- 733 residues
- Chains
- 3
- 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, ZN
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 57% 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 | 65% helix, 1% strand | Q04631 |
| B | Protein farnesyltransferase subunit beta (EC 2.5.1.58) | protein | 407 | 51% helix, 6% strand | Q02293 |
| C | Caged substrate | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · chains A, B, C
- ZN · Zinc ion · metal · chains B
- ACY · Acetic acid · additive · 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 | 645 | 0.75 | 0.81 | 66 | FPP |
| 2 | 100 | 0.75 | 0.96 | 25 | empty |
| 3 | 275 | 0.73 | 0.87 | 41 | empty |
| 4 | 203 | 0.60 | 0.81 | 28 | empty |
| 5 | 240 | 0.51 | 0.75 | 40 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3546 Ų buried · 66 hydrogen bonds · protein-protein
- B–C · 245 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 153 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3DPY · Protein farnesyltransferase complexed with FPP and caged TKCVIM substrate · 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 3DPY · PDBe 3DPY · UniProt Q04631 · UniProt Q02293
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