Research workbench
Crystal Structure of the cross-restricted T18A TCR and HLAB4201 bound to HIV-1 Gag TL9 peptide
Analyse Crystal Structure of the cross-restricted T18A TCR and HLAB4201 bound to HIV-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DZN
- Type
- protein
- Length
- 829 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.63
- Source
- Homo sapiens; Human immunodeficiency virus 1
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Gag-Pol polyprotein; beta chain T18A TCR…
- UniProt
- V6E0U6, P61769, P03367
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.63 · 5 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 277 | 26% helix, 40% strand | V6E0U6 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| C | Gag-Pol polyprotein | protein | 9 | 0% helix, 0% strand | P03367 |
| D | beta chain T18A TCR | protein | 241 | 7% helix, 51% strand | — |
| E | alpha chain T18A TCR | protein | 202 | 5% helix, 41% strand | — |
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.72 | 0.76 | 86 | empty |
| 2 | 481 | 0.68 | 0.79 | 52 | empty |
| 3 | 113 | 0.56 | 0.85 | 25 | empty |
| 4 | 130 | 0.49 | 0.79 | 28 | empty |
| 5 | 153 | 0.47 | 0.77 | 26 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2159 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1357 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 860 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 395 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 235 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7DZN · Crystal structure of the cross-restricted T18A TCR and HLAB4201 bound to HIV-1 gag TL9… · 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 0.98
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 V6E0U6
- Every structure of UniProt P61769
- Every structure of UniProt P03367
- Elsewhere: RCSB PDB 7DZN · PDBe 7DZN · UniProt V6E0U6 · UniProt P61769 · UniProt P03367
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