Research workbench
Rigor kinesin motor domain with an ordered neck-linker, docked on tubulin dimer, modelled into the 8A cryo-EM MAP of doublecortin- microtubules decorated with kinesin
Analyse Rigor kinesin motor domain with an ordered neck-linker, docked on tubulin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ATX
- 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-1D chain; Kinesin-1 heavy chain
- EC
- 3.6.5.6, 3.6.4.4
- UniProt
- Q6B856, Q2HJ86, Q2PQA9
- Ligands
- GDP, GTP
- Pockets
- 16 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tubulin beta-2B chain (EC 3.6.5.6) | protein | 426 | 44% helix, 14% strand | Q6B856 |
| B | Tubulin alpha-1D chain (EC 3.6.5.6) | protein | 429 | 42% helix, 14% strand | Q2HJ86 |
| C | Kinesin-1 heavy chain (EC 3.6.4.4) | protein | 309 | 33% helix, 28% strand | Q2PQA9 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- GTP · Guanosine-5'-triphosphate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.83 | 0.96 | 40 | GTP |
| 2 | 983 | 0.81 | 0.83 | 91 | empty |
| 3 | 60 | 0.70 | 0.96 | 22 | empty |
| 4 | 332 | 0.59 | 0.77 | 39 | empty |
| 5 | 280 | 0.55 | 0.76 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1718 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 318 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 245 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4ATX · Rigor kinesin motor domain with an ordered neck-linker, docked on tubulin dimer, modelled… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2PQA9 · AlphaFold monomer V2.0 prediction for kinesin-1 heavy chain (Q2PQA9) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q2HJ86
- Every structure of UniProt Q2PQA9
- Elsewhere: RCSB PDB 4ATX · PDBe 4ATX · UniProt Q6B856 · UniProt Q2HJ86 · UniProt Q2PQA9
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