MolNFT v1 · #167527 · protein
Cryo-EM structure of the C-terminal half of the PARKINSON'S disease- linked protein leucine rich repeat kinase 2 (LRRK2)
6VNO · Leucine-rich repeat SERINE/THREONINE-protein kinase 2: “Cryo-EM structure of the C-terminal half of the PARKINSON'S disease- linked protein leucine rich repeat…”. Electron microscopy, 2 ligands (GDP, MG), 20 pockets (best…
- PDB
- 6VNO
- Type
- protein
- Length
- 1,084 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine-rich repeat SERINE/THREONINE-protein kinase 2
- EC
- 2.7.11.1, 3.6.5.-
- UniProt
- Q5S007
- Ligands
- GDP, MG
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 1 distinct chain · 30% helix, 28% 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 | 1084 | 30% helix, 28% strand | Q5S007 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.75 | 0.77 | 65 | empty |
| 2 | 107 | 0.71 | 0.92 | 20 | empty |
| 3 | 346 | 0.70 | 0.83 | 51 | empty |
| 4 | 594 | 0.69 | 0.78 | 58 | empty |
| 5 | 227 | 0.65 | 0.83 | 24 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6VNO · Cryo-EM structure of the C-terminal half of the Parkinson's Disease-linked protein… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.92
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 Q5S007
- Elsewhere: RCSB PDB 6VNO · PDBe 6VNO · UniProt Q5S007
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