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1.9A crystal structure of the GTPase domain of PARKINSON'S disease- associated protein LRRK2 carrying R1398H
Analyse 1.9A crystal structure of the GTPase domain of PARKINSON'S disease- associated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XAF
- Type
- protein
- Length
- 346 residues
- Chains
- 2
- Method
- x-ray diffraction
- 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
- 4 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 25% 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 | 172 | 44% helix, 26% strand | Q5S007 |
| B | Leucine-rich repeat SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1, 3.6.5.-) | protein | 174 | 41% helix, 24% strand | Q5S007 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.43 | 0.77 | 21 | empty |
| 2 | 69 | 0.33 | 0.76 | 17 | empty |
| 3 | 81 | 0.33 | 0.75 | 18 | empty |
| 4 | 51 | 0.32 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2631 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 6XAF · 1.9A crystal structure of the GTPase domain of Parkinson's disease-associated 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 0.73
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 6XAF · PDBe 6XAF · UniProt Q5S007
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