Research workbench
HA1.7, a MHC class II restricted TCR specific for haemagglutinin
Analyse HA1.7, a MHC class II restricted TCR specific for haemagglutinin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GKZ
- Type
- protein
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha chain of class II TCR; Beta chain of class II TCR
- Ligands
- TAM, SO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha chain of class II TCR | protein | 202 | 4% helix, 43% strand | — |
| B | Beta chain of class II TCR | protein | 241 | 7% helix, 49% strand | — |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
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 | 892 | 0.75 | 0.78 | 76 | empty |
| 2 | 152 | 0.44 | 0.75 | 26 | empty |
| 3 | 76 | 0.37 | 0.77 | 19 | empty |
| 4 | 68 | 0.35 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2066 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4GKZ · HA1.7, a MHC class II restricted TCR specific for haemagglutinin · 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 4GKZ · PDBe 4GKZ
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