MolNFT v1 · #91313 · protein
Crystal structure of the human BTN3A1 ectodomain in complex with the 20.1 single chain antibody
4F9L · Butyrophilin subfamily 3 member A1: “Crystal structure of the human BTN3A1 ectodomain in complex with the 20.1 single chain antibody”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.45). MolNFT v1 #91313 on…
- 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
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