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
- 2VLR
- Type
- protein
- Length
- 1,648 residues
- Chains
- 10
- 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
- 20 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 25% helix, 39% strand | P01892 |
| B, G | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, H | Flu matrix peptide | protein | 9 | 0% helix, 0% strand | — |
| D, I | JM22 TCR alpha chain | protein | 199 | 4% helix, 45% strand | — |
| E, J | JM22 TCR beta chain | protein | 240 | 6% helix, 48% strand | — |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.72 | 0.79 | 85 | empty |
| 2 | 482 | 0.70 | 0.80 | 67 | empty |
| 3 | 641 | 0.68 | 0.77 | 53 | empty |
| 4 | 598 | 0.67 | 0.77 | 55 | empty |
| 5 | 508 | 0.65 | 0.77 | 76 | empty |
Interfaces
16 interfaces between chains.
- I–J · 2253 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 2242 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1427 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1425 Ų buried · 21 hydrogen bonds · protein-protein
- D–I · 896 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 2VLR · The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are… · the same entry in another collection · chain J against J, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain G 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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 2VLR · PDBe 2VLR · UniProt P01892 · UniProt P61769
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