Research workbench
Crystal structure of human LGI1 eptp-ADAM22 complex
Analyse Crystal structure of human LGI1 eptp-ADAM22 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y2Z
- Type
- protein
- Length
- 4,820 residues
- Chains
- 12
- 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, FUC, BMA, CA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 19% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Disintegrin and metalloproteinase domain-containing protein 22 | protein | 482 | 22% helix, 21% strand | Q9P0K1 |
| C | Disintegrin and metalloproteinase domain-containing protein 22 | protein | 473 | 24% helix, 21% strand | Q9P0K1 |
| E | Disintegrin and metalloproteinase domain-containing protein 22 | protein | 467 | 23% helix, 20% strand | Q9P0K1 |
| G | Disintegrin and metalloproteinase domain-containing protein 22 | protein | 462 | 24% helix, 20% strand | Q9P0K1 |
| I | Disintegrin and metalloproteinase domain-containing protein 22 | protein | 481 | 23% helix, 21% strand | Q9P0K1 |
| K | Disintegrin and metalloproteinase domain-containing protein 22 | protein | 486 | 22% helix, 23% strand | Q9P0K1 |
| B, D, F, J, L | Leucine-rich glioma-inactivated protein 1 | protein | 328 | 0% helix, 65% strand | O95970 |
| H | Leucine-rich glioma-inactivated protein 1 | protein | 329 | 0% helix, 64% strand | O95970 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains B, D, F, H, J, L
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains B, D, F, H, J, L
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 24 copies · chains A, C, E, G, I, K, B, D, F, H, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.82 | 0.83 | 108 | empty |
| 2 | 784 | 0.80 | 0.83 | 76 | empty |
| 3 | 737 | 0.79 | 0.83 | 82 | empty |
| 4 | 890 | 0.79 | 0.81 | 65 | empty |
| 5 | 876 | 0.78 | 0.81 | 77 | empty |
Interfaces
17 interfaces between chains.
- I–J · 1119 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1110 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1105 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1101 Ų buried · 11 hydrogen bonds · protein-protein
- K–L · 1093 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 126 disulfide, 13 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 5Y2Z · Crystal structure of human LGI1 EPTP-ADAM22 complex · the same entry in another collection · chain L against L, 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 Q9P0K1
- Every structure of UniProt O95970
- Elsewhere: RCSB PDB 5Y2Z · PDBe 5Y2Z · UniProt Q9P0K1 · UniProt O95970
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