MolNFT v2 · #227448 · protein
Autoinhibited full-length LRRK2(I2020T) on microtubules with MLi-2
9CHO · Leucine-rich repeat serine/threonine-protein kinase 2: “Autoinhibited full-length LRRK2(I2020T) on microtubules with MLi-2”. Electron microscopy at 7.8, 2 ligands (GDP, A1N), 20 pockets (best druggability 0.82). MolNFT v2 #227448 on…
- PDB
- 9CHO
- Type
- protein
- Length
- 1,792 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 7.8
- Source
- Homo sapiens
- Molecule
- Leucine-rich repeat serine/threonine-protein kinase 2
- EC
- 2.7.11.1, 3.6.5.-
- UniProt
- Q5S007
- Ligands
- GDP, A1N
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 7.8 · 1 distinct chain · 29% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine-rich repeat serine/threonine-protein kinase 2 (EC 2.7.11.1, 3.6.5.-) | protein | 1792 | 29% helix, 16% strand | Q5S007 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- A1N · (2~{R},6~{S})-2,6-dimethyl-4-[6-[5-(1-methylcyclopropyl)oxy-1~{H}-indazol-3-yl]pyrimidin-4-yl]morpholine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.82 | 0.85 | 100 | empty |
| 2 | 1016 | 0.77 | 0.79 | 59 | empty |
| 3 | 1127 | 0.76 | 0.78 | 107 | empty |
| 4 | 246 | 0.75 | 0.89 | 39 | empty |
| 5 | 254 | 0.74 | 0.88 | 46 | empty |
Compared structures
- Q5S007 · AlphaFold monomer V2.0 prediction for leucine-rich repeat SERINE/THREONINE-protein kinase… · a predicted model of the same protein · chain A against A, TM-score 0.61
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 Q5S007
- Elsewhere: RCSB PDB 9CHO · PDBe 9CHO · UniProt Q5S007
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