Research workbench
Crystal structure of drosophila melanogaster kinesin-1 motor domain dimer
Analyse Crystal structure of drosophila melanogaster kinesin-1 motor domain dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y5W
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin heavy chain
- UniProt
- P17210
- Ligands
- ADP, MG
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kinesin heavy chain | protein | 334 | 31% helix, 25% strand | P17210 |
| B | Kinesin heavy chain | protein | 330 | 30% helix, 28% strand | P17210 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.64 | 0.77 | 56 | empty |
| 2 | 158 | 0.54 | 0.81 | 31 | MG |
| 3 | 145 | 0.52 | 0.80 | 34 | MG |
| 4 | 71 | 0.46 | 0.83 | 17 | empty |
| 5 | 216 | 0.46 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 530 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2Y5W · Crystal structure of Drosophila melanogaster kinesin-1 motor domain dimer · the same entry in another collection · chain A against A, TM-score 1.00
- P17210 · AlphaFold monomer V2.0 prediction for kinesin heavy chain (P17210) · 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 P17210
- Elsewhere: RCSB PDB 2Y5W · PDBe 2Y5W · UniProt P17210
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.