MolNFT v1 · #51917 · protein
The structural dynamics and energetics of an immunodominant T-cell receptor are programmed by its vbeta domain
2VLK · HLA class I histocompatibility antigen, a-2 alpha chain: “The structural dynamics and energetics of an immunodominant T-cell receptor are programmed by its vbeta domain”. X-ray diffraction, 12 pockets (best druggability 0.73).…
- PDB
- 2VLK
- Type
- protein
- Length
- 824 residues
- Chains
- 5
- 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
- 12 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 25% helix, 38% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Flu matrix peptide | protein | 9 | 0% helix, 0% strand | — |
| D | JM22 TCR alpha chain | protein | 199 | 2% helix, 45% strand | — |
| E | JM22 TCR beta chain | protein | 240 | 6% helix, 50% strand | — |
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 | 1053 | 0.73 | 0.77 | 92 | empty |
| 2 | 655 | 0.69 | 0.77 | 53 | empty |
| 3 | 192 | 0.57 | 0.80 | 30 | empty |
| 4 | 188 | 0.51 | 0.78 | 36 | empty |
| 5 | 119 | 0.44 | 0.77 | 25 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2231 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1374 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 826 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 480 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 253 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 2VLK · The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are… · 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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 2VLK · PDBe 2VLK · UniProt P01892 · UniProt P61769
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