Research workbench
Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in epstein-barr virus
Analyse Genetic and structural basis for selection of a ubiquitous 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
- 3O4L
- Type
- protein
- Length
- 825 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; BSLF2/BMLF1 protein; T-cell receptor, alpha…
- UniProt
- Q8WLS4, P61769, A7UMS0
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 27% helix, 40% strand | Q8WLS4 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | BSLF2/BMLF1 protein | protein | 9 | 0% helix, 0% strand | A7UMS0 |
| D | T-cell receptor, alpha chain | protein | 195 | 2% helix, 44% strand | — |
| E | T-cell receptor, beta chain | protein | 245 | 7% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, E, D
- GOL · Glycerol · additive · 11 copies · chains A, B, D, C, E
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.73 | 0.76 | 87 | GOL |
| 2 | 563 | 0.67 | 0.77 | 55 | empty |
| 3 | 190 | 0.62 | 0.83 | 32 | empty |
| 4 | 199 | 0.49 | 0.76 | 30 | empty |
| 5 | 56 | 0.44 | 0.83 | 17 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2201 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1399 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 758 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 577 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 427 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3O4L · Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in… · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q8WLS4
- Every structure of UniProt P61769
- Every structure of UniProt A7UMS0
- Elsewhere: RCSB PDB 3O4L · PDBe 3O4L · UniProt Q8WLS4 · UniProt P61769 · UniProt A7UMS0
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