Research workbench
Dimeric structure of LRRK2 GTPase domain
Analyse Dimeric structure of LRRK2 GTPase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OJF
- Type
- protein
- Length
- 374 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
- UniProt
- Q5S007
- Ligands
- GDP, MG
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine-rich repeat SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1) | protein | 188 | 38% helix, 22% strand | Q5S007 |
| B | Leucine-rich repeat SERINE/THREONINE-protein kinase 2 (EC 2.7.11.1) | protein | 186 | 38% helix, 22% strand | Q5S007 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 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 | 67 | 0.48 | 0.84 | 16 | empty |
| 2 | 100 | 0.45 | 0.80 | 21 | empty |
| 3 | 119 | 0.41 | 0.76 | 25 | empty |
| 4 | 102 | 0.35 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3137 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
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 6OJF · PDBe 6OJF · UniProt Q5S007
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