Research workbench
HLA-B*27:05 presenting an HIV-1 7MER peptide
Analyse HLA-B*27:05 presenting an HIV-1 7MER peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VQY
- Type
- protein
- Length
- 762 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; 7-mer peptide
- UniProt
- O78189, P61769
- Ligands
- ARG
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | MHC class I antigen | protein | 275 | 27% helix, 40% strand | O78189 |
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| G, F | 7-mer peptide | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- ARG · Arginine · ligand · 3 copies · chains A, C, D
- GOL · Glycerol · additive · 2 copies · chains A, F, C, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.77 | 0.79 | 91 | ARG |
| 2 | 710 | 0.73 | 0.79 | 63 | empty |
| 3 | 477 | 0.68 | 0.79 | 49 | empty |
| 4 | 187 | 0.67 | 0.85 | 30 | ARG, GOL |
| 5 | 192 | 0.66 | 0.85 | 26 | ARG, GOL |
Interfaces
7 interfaces between chains.
- C–D · 1306 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1252 Ų buried · 19 hydrogen bonds · protein-protein
- C–G · 660 Ų buried · 12 hydrogen bonds · protein-protein
- A–F · 656 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 425 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
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 O78189
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6VQY · PDBe 6VQY · UniProt O78189 · UniProt P61769
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