MolNFT v1 · #85915 · protein
Model of human kinesin-5 motor domain (3HQD) and mammalian tubulin heterodimer (1JFF) docked into the 9.7-ångström cryo-EM MAP of microtubule-bound kinesin-5 motor domain in the ampppnp state.
4AQV · Tubulin alpha-1D chain: “Model of human kinesin-5 motor domain (3HQD) and mammalian tubulin heterodimer (1JFF) docked into the…”. Electron microscopy, 5 ligands (GTP, GDP, TA1), 4 pockets (best druggability 0.42). MolNFT v1 #85915…
- PDB
- 4AQV
- Type
- protein
- Length
- 1,199 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1D chain; Tubulin beta-2B chain; Kinesin-like protein KIF11
- UniProt
- Q2HJ86, Q6B856, P52732
- Ligands
- GTP, GDP, TA1, ANP, MG
- Pockets
- 4 · best druggability 0.42
Structure
electron microscopy · 3 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha-1D chain | protein | 412 | 0% helix, 0% strand | Q2HJ86 |
| B | Tubulin beta-2B chain | protein | 426 | 0% helix, 0% strand | Q6B856 |
| C | Kinesin-like protein KIF11 | protein | 361 | 0% helix, 0% strand | P52732 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- TA1 · Taxol · ligand · chains B
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.42 | 0.73 | 32 | empty |
| 2 | 119 | 0.39 | 0.73 | 35 | empty |
| 3 | 88 | 0.35 | 0.73 | 24 | empty |
| 4 | 82 | 0.34 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4AQV · Model of human kinesin-5 motor domain (3HQD) and mammalian tubulin heterodimer (1JFF)… · 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 Q2HJ86
- Every structure of UniProt Q6B856
- Every structure of UniProt P52732
- Elsewhere: RCSB PDB 4AQV · PDBe 4AQV · UniProt Q2HJ86 · UniProt Q6B856 · UniProt P52732
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