Research workbench
Structural basis for degenerate recognition of HIV peptide variants by cytotoxic lymphocyte, variant SL9, monoclinic crystal
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
- 1T21
- Type
- protein
- Length
- 383 residues
- Chains
- 3
- 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; Gag peptide
- UniProt
- P01892, P01884
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 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 | 669 | 0.68 | 0.77 | 60 | empty |
| 2 | 61 | 0.40 | 0.80 | 15 | empty |
| 3 | 62 | 0.40 | 0.80 | 17 | empty |
| 4 | 63 | 0.33 | 0.76 | 16 | empty |
| 5 | 63 | 0.32 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1344 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 845 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1T21 · 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 1T21 · PDBe 1T21 · UniProt P01892 · UniProt P01884
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