Research workbench
Crystal structure of the motor protein ksp in complex with ADP and monastrol
Analyse Crystal structure of the motor protein ksp in complex with ADP and monastrol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q0B
- Type
- protein
- Length
- 666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like protein KIF11
- UniProt
- P52732
- Ligands
- ADP, NAT, MG
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kinesin-like protein KIF11 | protein | 331 | 35% helix, 32% strand | P52732 |
| B | Kinesin-like protein KIF11 | protein | 335 | 33% helix, 31% strand | P52732 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAT · Ethyl 4-(3-hydroxyphenyl)-6-methyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.69 | 0.74 | 78 | empty |
| 2 | 286 | 0.64 | 0.81 | 52 | MG, ADP, NAT |
| 3 | 394 | 0.63 | 0.78 | 35 | empty |
| 4 | 295 | 0.60 | 0.79 | 30 | empty |
| 5 | 164 | 0.59 | 0.82 | 24 | NAT |
Interfaces
1 interface between chains.
- A–B · 218 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1Q0B · Crystal structure of the motor protein KSP in complex with ADP and monastrol · the same entry in another collection · chain A against A, TM-score 1.00
- P52732 · AlphaFold monomer V2.0 prediction for kinesin-like protein KIF11 (P52732) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 1Q0B · PDBe 1Q0B · UniProt P52732
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