Research workbench
The crystal structure of the minimal core domain of the microtubule depolymerizer KIF2C complexed with ADP-mg-alfx
Analyse The crystal structure of the minimal core domain of the microtubule… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XJA
- Type
- protein
- Length
- 669 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like protein KIF2C
- UniProt
- Q922S8
- Ligands
- ADP, AF3, MG
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kinesin-like protein KIF2C | protein | 337 | 34% helix, 30% strand | Q922S8 |
| B | Kinesin-like protein KIF2C | protein | 332 | 36% helix, 30% strand | Q922S8 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- AF3 · Aluminum fluoride · 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
14 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.75 | 0.90 | 42 | empty |
| 2 | 154 | 0.48 | 0.78 | 22 | empty |
| 3 | 145 | 0.47 | 0.77 | 22 | empty |
| 4 | 121 | 0.45 | 0.77 | 20 | empty |
| 5 | 125 | 0.44 | 0.77 | 32 | MG, ADP, AF3 |
Interfaces
1 interface between chains.
- A–B · 1054 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5XJA · The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C… · the same entry in another collection · chain A against A, TM-score 1.00
- Q922S8 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF2C (Q922S8) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 Q922S8
- Elsewhere: RCSB PDB 5XJA · PDBe 5XJA · UniProt Q922S8
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