MolNFT v1 · #88082 · protein
Pseudo-atomic model of microtubule-bound human kinesin-5 motor domain in the ADP state, based on cryo-electron microscopy experiment.
4CK5 · Tubulin alpha-1D chain: “Pseudo-atomic model of microtubule-bound human kinesin-5 motor domain in the ADP state, based on…”. Electron microscopy, 5 ligands (GTP, GDP, TA1), 3 pockets (best druggability 0.43). MolNFT v1 #88082 on…
- PDB
- 4CK5
- Type
- protein
- Length
- 1,188 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, ADP, MG
- Pockets
- 3 · best druggability 0.43
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 | 350 | 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
- ADP · Adenosine-5'-diphosphate · ligand · chains C
- MG · Magnesium ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.43 | 0.72 | 38 | empty |
| 2 | 105 | 0.38 | 0.73 | 26 | empty |
| 3 | 67 | 0.32 | 0.73 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 81 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 73 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4CK5 · Pseudo-atomic model of microtubule-bound human kinesin-5 motor domain in the ADP state… · the same entry in another collection · chain B against B, 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 4CK5 · PDBe 4CK5 · UniProt Q2HJ86 · UniProt Q6B856 · UniProt P52732
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