Research workbench
Crystal structure of LRIM1 leucine-rich repeat domain
Analyse Crystal structure of LRIM1 leucine-rich repeat domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O53
- Type
- protein
- Length
- 630 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein LRIM1
- UniProt
- Q7Q5N3
- Ligands
- NAG, CO
- Pockets
- 5 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein LRIM1 | protein | 316 | 21% helix, 25% strand | Q7Q5N3 |
| B | Protein LRIM1 | protein | 314 | 20% helix, 24% strand | Q7Q5N3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.49 | 0.77 | 22 | empty |
| 2 | 131 | 0.46 | 0.78 | 19 | empty |
| 3 | 165 | 0.45 | 0.75 | 28 | empty |
| 4 | 81 | 0.36 | 0.76 | 18 | empty |
| 5 | 59 | 0.31 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 411 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3O53 · Crystal Structure of LRIM1 leucine-rich repeat domain · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7Q5N3
- Elsewhere: RCSB PDB 3O53 · PDBe 3O53 · UniProt Q7Q5N3
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