Research workbench
Nucleotide-free kinesin motor domain in complex with tubulin and a darpin
Analyse Nucleotide-free kinesin motor domain in complex with tubulin and a darpin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LNU
- Type
- protein
- Length
- 1,331 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha chain; Tubulin beta chain; Designed ankyrin repeat protein (darpin) D1…
- UniProt
- P33176
- Ligands
- GTP, GDP, MG, SO4
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin alpha chain | protein | 434 | 44% helix, 18% strand | — |
| B | Tubulin beta chain | protein | 431 | 48% helix, 18% strand | — |
| D | Designed ankyrin repeat protein (darpin) D1 | protein | 157 | 54% helix, 0% strand | — |
| K | Kinesin-1 heavy chain | protein | 309 | 32% helix, 28% strand | P33176 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · chains B
- MG · Magnesium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, D, K
- GOL · Glycerol · additive · 4 copies · chains B, D, A, K
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.83 | 0.84 | 89 | MES, SO4, GOL |
| 2 | 422 | 0.77 | 0.86 | 53 | GTP, MG |
| 3 | 475 | 0.68 | 0.79 | 48 | SO4 |
| 4 | 303 | 0.63 | 0.80 | 41 | SO4 |
| 5 | 178 | 0.61 | 0.83 | 33 | GDP |
Interfaces
4 interfaces between chains.
- A–B · 1413 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 935 Ų buried · 9 hydrogen bonds · protein-protein
- A–K · 808 Ų buried · 8 hydrogen bonds · protein-protein
- B–K · 684 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4LNU · Nucleotide-free kinesin motor domain in complex with tubulin and a DARPin · the same entry in another collection · chain A against A, 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 P33176
- Elsewhere: RCSB PDB 4LNU · PDBe 4LNU · UniProt P33176
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