MolNFT v1 · #66439 · protein
Human kinesin EG5 motor domain in complex with amppnp and MG2+
3HQD · Kinesin-like protein KIF11: “Human kinesin EG5 motor domain in complex with amppnp and MG2+”. X-ray diffraction, 3 ligands (ANP, MG, PO4), 8 pockets (best druggability 0.68). MolNFT v1 #66439 on GenesisL1: 3D structure, binding…
- PDB
- 3HQD
- Type
- protein
- Length
- 700 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kinesin-like protein KIF11
- UniProt
- P52732
- Ligands
- ANP, MG, PO4
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kinesin-like protein KIF11 | protein | 350 | 33% helix, 31% strand | P52732 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.68 | 0.80 | 64 | ANP, MG |
| 2 | 335 | 0.66 | 0.81 | 40 | empty |
| 3 | 296 | 0.64 | 0.81 | 36 | empty |
| 4 | 317 | 0.62 | 0.79 | 45 | empty |
| 5 | 360 | 0.62 | 0.78 | 61 | ANP, MG |
Interfaces
1 interface between chains.
- A–B · 534 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3HQD · Human kinesin Eg5 motor domain in complex with AMPPNP and Mg2+ · 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 3HQD · PDBe 3HQD · UniProt P52732
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