MolNFT v1 · #167581 · protein
Cryo-EM structure of the C-terminal half of the PARKINSON'S disease- linked protein leucine rich repeat kinase 2 (LRRK2)
6VP6 · 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
- 6VP6
- Type
- protein
- Length
- 1,668 residues
- Chains
- 3
- 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 0.81
Structure
electron microscopy · 3 distinct chains · 25% helix, 33% 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 |
| B | Leucine-rich repeat SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 3.6.5.-) | protein | 265 | 25% helix, 27% strand | Q5S007 |
| C | Leucine-rich repeat SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 3.6.5.-) | protein | 319 | 7% helix, 56% 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.81 | 0.82 | 112 | empty |
| 2 | 914 | 0.79 | 0.82 | 71 | empty |
| 3 | 456 | 0.72 | 0.82 | 56 | empty |
| 4 | 534 | 0.72 | 0.80 | 67 | empty |
| 5 | 108 | 0.71 | 0.92 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1084 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 999 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6VP6 · 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 C against A, TM-score 0.98
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 6VP6 · PDBe 6VP6 · UniProt Q5S007
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