Research workbench
X-ray structure of mitotic kinesin-5 (ksp, KIF11, EG5)IN complex with the hexahydro-2H-PYRANO[3,2-C]QUINOLINE emd 534085
Analyse X-ray structure of mitotic kinesin-5 (ksp, KIF11, EG5)IN complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L9H
- Type
- protein
- Length
- 662 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like protein KIF11
- UniProt
- P52732
- Ligands
- ADP, EMQ
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kinesin-like protein KIF11 | protein | 331 | 33% helix, 32% strand | P52732 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- EMQ · 1-[2-(dimethylamino)ethyl]-3-{[(2R,4aS,5R,10bS)-5-phenyl-9-(trifluoromethyl)-3,4,4a,5,6,10b-hexahydro-2H-pyrano[3,2-c]quinolin-2-yl]methyl}urea · ligand · 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 | 1011 | 0.81 | 0.82 | 127 | ADP, EMQ |
| 2 | 309 | 0.60 | 0.78 | 31 | empty |
| 3 | 295 | 0.57 | 0.77 | 28 | empty |
| 4 | 102 | 0.37 | 0.75 | 29 | empty |
| 5 | 110 | 0.36 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 895 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3L9H · X-ray structure of mitotic kinesin-5 (KSP, KIF11, Eg5)in complex with the… · 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 3L9H · PDBe 3L9H · UniProt P52732
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