Research workbench
Crystal structure of the KIF1A motor domain complexed with ADP-mg-alfx
Analyse Crystal structure of the KIF1A motor domain complexed with ADP-mg-alfx in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VFX
- Type
- protein
- Length
- 323 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
- AF3, ADP, MG
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 29% 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 | 323 | 30% helix, 29% strand | P33173, P28738 |
Ligands and binding sites
- AF3 · Aluminum fluoride · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · 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 | 231 | 0.61 | 0.81 | 23 | empty |
| 2 | 248 | 0.53 | 0.76 | 39 | MG, AF3, ADP |
| 3 | 69 | 0.32 | 0.75 | 16 | empty |
Compared structures
- 1VFX · Crystal Structure of the Kif1A Motor Domain Complexed With ADP-Mg-AlFx · 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 0.98
- 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 0.89
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 1VFX · PDBe 1VFX · UniProt P33173 · UniProt P28738
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