MolNFT v1 · #159263 · protein
Monomeric kinesin-1 motor domain in no-nucleotide state bound to gmpcpp-stabilized microtubule
6OJQ · Tubulin beta-2B chain: “Monomeric kinesin-1 motor domain in no-nucleotide state bound to gmpcpp-stabilized microtubule”. Electron microscopy, 3 ligands (G2P, GTP, MG), 15 pockets (best druggability 0.83). MolNFT v1 #159263 on…
- PDB
- 6OJQ
- Type
- protein
- Length
- 1,164 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin beta-2B chain; Tubulin alpha-1B chain; Kinesin-1 heavy chain
- UniProt
- Q6B856, P81947, P33176
- Ligands
- G2P, GTP, MG
- Pockets
- 15 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Tubulin beta-2B chain | protein | 426 | 47% helix, 18% strand | Q6B856 |
| A | Tubulin alpha-1B chain | protein | 428 | 47% helix, 14% strand | P81947 |
| K | Kinesin-1 heavy chain | protein | 310 | 33% helix, 27% strand | P33176 |
Ligands and binding sites
- G2P · Phosphomethylphosphonic acid guanylate ester · ligand · chains B
- GTP · Guanosine-5'-triphosphate · ligand · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.83 | 0.96 | 40 | GTP, MG |
| 2 | 1168 | 0.82 | 0.83 | 123 | empty |
| 3 | 319 | 0.68 | 0.82 | 41 | G2P, MG |
| 4 | 337 | 0.66 | 0.81 | 52 | empty |
| 5 | 218 | 0.54 | 0.78 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–A · 2016 Ų buried · 33 hydrogen bonds · protein-protein
- A–K · 856 Ų buried · 7 hydrogen bonds · protein-protein
- B–K · 655 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6OJQ · Monomeric kinesin-1 motor domain in no-nucleotide state bound to GMPCPP-stabilized… · the same entry in another collection · chain B against B, TM-score 1.00
- P33176 · AlphaFold monomer V2.0 prediction for kinesin-1 heavy chain (P33176) · a predicted model of the same protein · chain K against A, TM-score 0.92
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 Q6B856
- Every structure of UniProt P81947
- Every structure of UniProt P33176
- Elsewhere: RCSB PDB 6OJQ · PDBe 6OJQ · UniProt Q6B856 · UniProt P81947 · UniProt P33176
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