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Structural basis for degenerate recognition of HIV peptide variants by cytotoxic lymphocyte, variant SL9-5V
Analyse Structural basis for degenerate recognition of HIV peptide variants by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T1Y
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- HLA class I histocompatibility antigen, A-2 alpha chain; Beta-2-microglobulin; Gag peptide
- UniProt
- P01892, P01884
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · resolution 2 · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, A-2 alpha chain | protein | 275 | 27% helix, 40% strand | P01892 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01884 |
| C | Gag peptide | protein | 9 | 0% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.68 | 0.77 | 58 | empty |
| 2 | 65 | 0.42 | 0.81 | 17 | empty |
| 3 | 77 | 0.40 | 0.79 | 20 | empty |
| 4 | 59 | 0.31 | 0.76 | 16 | empty |
| 5 | 69 | 0.31 | 0.74 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1342 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 855 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1T1Y · Structural basis for degenerate recognition of HIV peptide variants by cytotoxic… · the same entry in another collection · chain A against A, TM-score 1.00
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 P01884
- Elsewhere: RCSB PDB 1T1Y · PDBe 1T1Y · UniProt P01892 · UniProt P01884
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