Research workbench
Crystal structure of LRIM1/APL1C complex
Analyse Crystal structure of LRIM1/APL1C complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OJA
- Type
- protein
- Length
- 1,016 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine-rich immune molecule 1; Anopheles plasmodium-responsive leucine-rich repeat…
- UniProt
- Q7Q5N3
- Ligands
- NAG, MAN
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine-rich immune molecule 1 | protein | 482 | 44% helix, 16% strand | Q7Q5N3 |
| B | Anopheles plasmodium-responsive leucine-rich repeat protein 1 | protein | 534 | 31% helix, 15% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.69 | 0.78 | 41 | empty |
| 2 | 762 | 0.68 | 0.76 | 82 | empty |
| 3 | 482 | 0.63 | 0.77 | 41 | empty |
| 4 | 214 | 0.49 | 0.75 | 31 | empty |
| 5 | 199 | 0.47 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 5258 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 3OJA · Crystal structure of LRIM1/APL1C complex · 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 3OJA · PDBe 3OJA · UniProt Q7Q5N3
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