Research workbench
Crystal structure of the human BTN3A1 ectodomain in complex with the 20.1 single chain antibody
Analyse Crystal structure of the human BTN3A1 ectodomain in complex with the 20.1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F9L
- Type
- protein
- Length
- 891 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Butyrophilin subfamily 3 member A1; 20.1 anti-BTN3A1 antibody fragment
- UniProt
- O00481
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Butyrophilin subfamily 3 member A1 | protein | 214 | 6% helix, 54% strand | O00481 |
| D, C | 20.1 anti-BTN3A1 antibody fragment | protein | 232 | 4% helix, 47% strand | — |
| B | Butyrophilin subfamily 3 member A1 | protein | 213 | 6% helix, 52% strand | O00481 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.45 | 0.75 | 25 | empty |
| 2 | 153 | 0.42 | 0.75 | 29 | empty |
| 3 | 63 | 0.41 | 0.81 | 13 | empty |
| 4 | 104 | 0.40 | 0.76 | 16 | empty |
| 5 | 107 | 0.38 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 852 Ų buried · 16 hydrogen bonds · protein-protein
- C–B · 624 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 622 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4F9L · Crystal Structure of the Human BTN3A1 Ectodomain in Complex with the 20.1 Single Chain… · the same entry in another collection · chain A against A, TM-score 1.00
- O00481 · AlphaFold monomer V2.0 prediction for butyrophilin subfamily 3 member A1 (O00481) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O00481
- Elsewhere: RCSB PDB 4F9L · PDBe 4F9L · UniProt O00481
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.