MolNFT v1 · #18801 · protein
Crystal structure of the motor protein ksp in complex with ADP and monastrol
1Q0B · Kinesin-like protein KIF11: “Crystal structure of the motor protein ksp in complex with ADP and monastrol”. X-ray diffraction, 3 ligands (ADP, NAT, MG), 6 pockets (best druggability 0.69). MolNFT v1 #18801 on GenesisL1: 3D…
- 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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