Research workbench
The structural dynamics and energetics of an immunodominant T-cell receptor are programmed by its vbeta domain
Analyse The structural dynamics and energetics of an immunodominant T-cell receptor are… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VLL
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; Flu matrix…
- UniProt
- P01892, P61769
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 28% helix, 40% strand | P01892 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Flu matrix peptide | protein | 9 | 0% helix, 0% strand | — |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.67 | 0.77 | 62 | empty |
| 2 | 474 | 0.66 | 0.78 | 55 | empty |
| 3 | 112 | 0.45 | 0.78 | 22 | empty |
| 4 | 110 | 0.43 | 0.78 | 18 | empty |
| 5 | 57 | 0.41 | 0.82 | 17 | empty |
Interfaces
4 interfaces between chains.
- D–E · 1376 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1342 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 843 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 834 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2VLL · The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are… · the same entry in another collection · chain F against F, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 2VLL · PDBe 2VLL · UniProt P01892 · UniProt P61769
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