Research workbench
Crystal structure of the HY19.3 type II nkt TCR
Analyse Crystal structure of the HY19.3 type II nkt TCR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ELK
- Type
- protein
- Length
- 886 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HY19.3 TCR alpha chain (mouse variable domain, human constant domain); HY19.3 TCR beta…
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HY19.3 TCR alpha chain (mouse variable domain, human constant domain) | protein | 199 | 5% helix, 49% strand | — |
| B | HY19.3 TCR beta chain (mouse variable domain, human constant domain) | protein | 242 | 7% helix, 50% strand | — |
| C | HY19.3 TCR alpha chain (mouse variable domain, human constant domain) | protein | 203 | 5% helix, 46% strand | — |
| D | HY19.3 TCR beta chain (mouse variable domain, human constant domain) | protein | 242 | 7% helix, 51% strand | — |
Ligands and binding sites
- FMT · Formic acid · additive · 7 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 5 copies · chains A, B
- MLI · Malonate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.72 | 0.75 | 75 | FMT |
| 2 | 389 | 0.64 | 0.79 | 45 | ACT, FMT |
| 3 | 320 | 0.56 | 0.76 | 47 | empty |
| 4 | 164 | 0.51 | 0.79 | 31 | empty |
| 5 | 92 | 0.37 | 0.76 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2209 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2172 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 905 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4ELK · Crystal structure of the Hy19.3 type II NKT TCR · 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 4ELK · PDBe 4ELK
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