Research workbench
Crystal structure of the KIF1A motor domain complexed with ADP-mg-VO4
Analyse Crystal structure of the KIF1A motor domain complexed with ADP-mg-VO4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VFZ
- Type
- protein
- Length
- 338 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (fusion protein consisting of kinesin-like protein KIF1A, kinesin heavy chain…
- UniProt
- P33173, P28738
- Ligands
- ADP, MG, VO4
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (fusion protein consisting of kinesin-like protein KIF1A, kinesin heavy chain isoform 5C and a his tag | protein | 338 | 35% helix, 28% strand | P33173, P28738 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- VO4 · Vanadate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.62 | 0.84 | 23 | empty |
| 2 | 204 | 0.51 | 0.77 | 38 | MG, ADP |
| 3 | 84 | 0.37 | 0.77 | 17 | empty |
Compared structures
- 1VFZ · Crystal Structure of the Kif1A Motor Domain Complexed With ADP-Mg-VO4 · the same entry in another collection · chain A against A, TM-score 1.00
- P33173 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF1A (P33173) · a predicted model of the same protein · chain A against A, TM-score 0.93
- P28738 · AlphaFold monomer V2.0 prediction for kinesin heavy chain isoform 5C (P28738) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P33173
- Every structure of UniProt P28738
- Elsewhere: RCSB PDB 1VFZ · PDBe 1VFZ · UniProt P33173 · UniProt P28738
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