MolNFT v1 · #180756 · protein
O6 variable lymphocyte receptor ectodomain bound to 3-HSO3-gal-4GLCNAC
7LA8: “O6 variable lymphocyte receptor ectodomain bound to 3-HSO3-gal-4GLCNAC”. X-ray diffraction, 4 ligands (SGA, BTN, NAG), 4 pockets (best druggability 0.72). MolNFT v1 #180756 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7LA8
- Type
- protein
- Length
- 344 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O6 variable lymphocyte receptor
- Ligands
- SGA, BTN, NAG, SO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | O6 variable lymphocyte receptor | protein | 172 | 17% helix, 17% strand | — |
Ligands and binding sites
- SGA · 3-O-sulfo-beta-D-galactopyranose · ligand · 2 copies · chains A, B
- BTN · Biotin · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.72 | 0.80 | 43 | empty |
| 2 | 64 | 0.31 | 0.75 | 14 | SGA |
| 3 | 58 | 0.30 | 0.75 | 14 | SGA |
| 4 | 54 | 0.27 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 479 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7LA8 · O6 variable lymphocyte receptor ectodomain bound to 3-HSO3-Gal-4GlcNAc · 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
- Elsewhere: RCSB PDB 7LA8 · PDBe 7LA8
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