Research workbench
HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes
Analyse HLA class I micropolymorphisms determine peptide-HLA landscape and dictate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U1H
- Type
- protein
- Length
- 386 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.59
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- HLA class I histocompatibility antigen, B-7 alpha chain; Beta-2-microglobulin; GAG protein
- UniProt
- P01889, P61769, Q70A36
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · resolution 1.59 · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-7 alpha chain | protein | 277 | 27% helix, 39% strand | P01889 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | GAG protein | protein | 9 | 0% helix, 0% strand | Q70A36 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, C, B
- GOL · Glycerol · additive · 3 copies · chains A, B, C
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 | 681 | 0.70 | 0.78 | 55 | EDO |
| 2 | 163 | 0.50 | 0.78 | 27 | empty |
| 3 | 105 | 0.42 | 0.77 | 22 | EDO |
| 4 | 53 | 0.38 | 0.80 | 14 | EDO |
| 5 | 67 | 0.31 | 0.75 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1306 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 898 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4U1H · HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential… · the same entry in another collection · chain A against A, TM-score 1.00
- P01889 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, B alpha… · a predicted model of the same protein · 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 P01889
- Every structure of UniProt P61769
- Every structure of UniProt Q70A36
- Elsewhere: RCSB PDB 4U1H · PDBe 4U1H · UniProt P01889 · UniProt P61769 · UniProt Q70A36
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