MolNFT v1 · #60990 · protein
Crystal structure of human fidgetin-like protein 1 in complex with ADP
3D8B: “Crystal structure of human fidgetin-like protein 1 in complex with ADP”. X-ray diffraction, 1 ligand (ADP), 11 pockets (best druggability 0.83). MolNFT v1 #60990 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3D8B
- Type
- protein
- Length
- 555 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fidgetin-like protein 1
- EC
- 3.6.4.-
- UniProt
- Q6PIW4
- Ligands
- ADP
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fidgetin-like protein 1 (EC 3.6.4.-) | protein | 281 | 54% helix, 12% strand | Q6PIW4 |
| B | Fidgetin-like protein 1 (EC 3.6.4.-) | protein | 274 | 56% helix, 11% strand | Q6PIW4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.83 | 0.86 | 84 | ADP |
| 2 | 413 | 0.67 | 0.80 | 38 | empty |
| 3 | 202 | 0.61 | 0.82 | 21 | empty |
| 4 | 114 | 0.56 | 0.84 | 18 | empty |
| 5 | 70 | 0.52 | 0.85 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1834 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3D8B · Crystal structure of human fidgetin-like protein 1 in complex with ADP · the same entry in another collection · chain A against A, TM-score 1.00
- Q6PIW4 · AlphaFold monomer V2.0 prediction for fidgetin-like protein 1 (Q6PIW4) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q6PIW4
- Elsewhere: RCSB PDB 3D8B · PDBe 3D8B · UniProt Q6PIW4
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