Research workbench
The mitotic kinesin EG5 in complex with mg-ADP and ispinesib
Analyse The mitotic kinesin EG5 in complex with mg-ADP and ispinesib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AP0
- Type
- protein
- Length
- 1,257 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like protein KIF11
- UniProt
- P52732
- Ligands
- ADP, G7X, MG, CL
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kinesin-like protein KIF11 | protein | 325 | 34% helix, 27% strand | P52732 |
| B | Kinesin-like protein KIF11 | protein | 312 | 35% helix, 29% strand | P52732 |
| C | Kinesin-like protein KIF11 | protein | 311 | 34% helix, 27% strand | P52732 |
| D | Kinesin-like protein KIF11 | protein | 309 | 35% helix, 28% strand | P52732 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, D, B, C
- G7X · Ispinesib mesilate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 6 copies · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.71 | 0.79 | 78 | MG, ADP, CL |
| 2 | 273 | 0.67 | 0.83 | 30 | G7X |
| 3 | 275 | 0.66 | 0.82 | 29 | G7X |
| 4 | 87 | 0.65 | 0.91 | 27 | empty |
| 5 | 234 | 0.65 | 0.83 | 26 | G7X |
Interfaces
4 interfaces between chains.
- A–B · 743 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 655 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 516 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4AP0 · The mitotic kinesin Eg5 in complex with Mg-ADP and ispinesib · the same entry in another collection · chain A against A, TM-score 1.00
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 P52732
- Elsewhere: RCSB PDB 4AP0 · PDBe 4AP0 · UniProt P52732
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