Research workbench
Structural and kinetic basis for heightened immunogenicity of T cell vaccines
Analyse Structural and kinetic basis for heightened immunogenicity of T cell vaccines in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BNR
- Type
- protein
- Length
- 829 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen; Beta-2-microglobulin; Synthetic peptide; T-cell…
- UniProt
- P01892, P61769, P01850
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen | protein | 276 | 26% helix, 39% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Synthetic peptide | protein | 9 | 0% helix, 0% strand | — |
| D | T-cell receptor alpha chain V region | protein | 203 | 6% helix, 47% strand | — |
| E | T-cell receptor beta chain C region | protein | 241 | 7% helix, 50% strand | P01850 |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.71 | 0.75 | 103 | empty |
| 2 | 578 | 0.67 | 0.77 | 56 | empty |
| 3 | 80 | 0.50 | 0.84 | 21 | empty |
| 4 | 118 | 0.50 | 0.80 | 23 | empty |
| 5 | 145 | 0.45 | 0.77 | 29 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2153 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1347 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 823 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 501 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 388 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2BNR · Structural and kinetic basis for heightened immunogenicity of T cell vaccines · the same entry in another collection · chain B against B, 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 0.98
- P01850 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 1 (P01850) · a predicted model of the same protein · chain E against A, TM-score 0.53
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
- Every structure of UniProt P01850
- Elsewhere: RCSB PDB 2BNR · PDBe 2BNR · UniProt P01892 · UniProt P61769 · UniProt P01850
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