Research workbench
Crystal structure of human LGI1-ADAM22 complex
Analyse Crystal structure of human LGI1-ADAM22 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y31
- Type
- protein
- Length
- 1,986 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disintegrin and metalloproteinase domain-containing protein 22; Leucine-rich…
- UniProt
- Q9P0K1, O95970
- Ligands
- NAG, CA
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Disintegrin and metalloproteinase domain-containing protein 22 | protein | 482 | 23% helix, 21% strand | Q9P0K1 |
| B, D | Leucine-rich glioma-inactivated protein 1 | protein | 511 | 4% helix, 50% strand | O95970 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.83 | 0.84 | 113 | empty |
| 2 | 1164 | 0.80 | 0.81 | 117 | empty |
| 3 | 962 | 0.80 | 0.81 | 91 | empty |
| 4 | 912 | 0.78 | 0.80 | 86 | empty |
| 5 | 307 | 0.71 | 0.84 | 42 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1075 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1012 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 929 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 375 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 306 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 disulfide, 11 glycan (disulfide, N-glycosylation, glycation).
Compared structures
- 5Y31 · Crystal structure of human LGI1-ADAM22 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9P0K1 · AlphaFold monomer V2.0 prediction for disintegrin and metalloproteinase domain-containing… · a predicted model of the same protein · chain A against A, TM-score 0.98
- O95970 · AlphaFold monomer V2.0 prediction for leucine-rich glioma-inactivated protein 1 (O95970) · a predicted model of the same protein · chain B against A, TM-score 0.80
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 Q9P0K1
- Every structure of UniProt O95970
- Elsewhere: RCSB PDB 5Y31 · PDBe 5Y31 · UniProt Q9P0K1 · UniProt O95970
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