Research workbench
Structure of XV19 VALPHA1-VBETA16 type-II natural killer T cell receptor
Analyse Structure of XV19 VALPHA1-VBETA16 type-II natural killer T cell receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EI6
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VALPHA1 XV19 type II natural killer T cell receptor (mouse variable domain, human…
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VALPHA1 XV19 type II natural killer T cell receptor (mouse variable domain, human constant domain) | protein | 202 | 5% helix, 47% strand | — |
| B | VBETA16 XV19 type II natural killer T cell receptor (mouse variable domain, human constant domain) | protein | 244 | 7% helix, 50% strand | — |
| C | VALPHA1 XV19 type II natural killer T cell receptor (mouse variable domain, human constant domain) | protein | 189 | 7% helix, 50% strand | — |
| D | VBETA16 XV19 type II natural killer T cell receptor (mouse variable domain, human constant domain) | protein | 241 | 6% helix, 51% strand | — |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.69 | 0.77 | 71 | empty |
| 2 | 480 | 0.65 | 0.77 | 62 | empty |
| 3 | 373 | 0.62 | 0.78 | 39 | empty |
| 4 | 127 | 0.49 | 0.79 | 34 | empty |
| 5 | 151 | 0.41 | 0.74 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2282 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2248 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1016 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4EI6 · Structure of XV19 Valpha1-Vbeta16 Type-II Natural Killer T cell receptor · 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 4EI6 · PDBe 4EI6
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