Research workbench
Crystal structure of HLA-B*5701 complex with an HIV-1 gag-derived epitope QW9 S3T variant
Analyse Crystal structure of HLA-B*5701 complex with an HIV-1 gag-derived epitope QW9… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R7Y
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Gln-ala-thr-gln-glu-val-lys-asn-TRP
- UniProt
- U6BR87, P61769
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 276 | 27% helix, 40% strand | U6BR87 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Gln-ala-thr-gln-glu-val-lys-asn-TRP | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 625 | 0.68 | 0.77 | 50 | GOL |
| 2 | 104 | 0.44 | 0.78 | 23 | empty |
| 3 | 89 | 0.42 | 0.79 | 17 | empty |
| 4 | 106 | 0.42 | 0.78 | 20 | empty |
| 5 | 68 | 0.36 | 0.77 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1312 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 929 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7R7Y · Crystal structure of HLA-B*5701 complex with an HIV-1 Gag-derived epitope QW9 S3T variant · 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 U6BR87
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 7R7Y · PDBe 7R7Y · UniProt U6BR87 · UniProt P61769
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.