Research workbench
Structure of new antigen receptor variable domain from sharks
Analyse Structure of new antigen receptor variable domain from sharks in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YWY
- Type
- protein
- Length
- 432 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- New antigen receptor variable domain
- UniProt
- A9CBG4
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | New antigen receptor variable domain | protein | 113 | 3% helix, 56% strand | A9CBG4 |
| B, D | New antigen receptor variable domain | protein | 103 | 3% helix, 59% strand | A9CBG4 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.58 | 0.89 | 23 | empty |
| 2 | 52 | 0.53 | 0.89 | 21 | empty |
| 3 | 251 | 0.52 | 0.75 | 33 | empty |
| 4 | 93 | 0.44 | 0.79 | 16 | empty |
| 5 | 76 | 0.35 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 948 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 623 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 609 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2YWY · Structure of new antigen receptor variable domain from sharks · 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
- Every structure of UniProt A9CBG4
- Elsewhere: RCSB PDB 2YWY · PDBe 2YWY · UniProt A9CBG4
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