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
- 4U1K
- Type
- protein
- Length
- 772 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-7 alpha chain; Beta-2-microglobulin; Protein nef
- UniProt
- P01889, P61769, Q90VG9
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, B-7 alpha chain | protein | 277 | 25% helix, 39% strand | P01889 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Protein nef | protein | 9 | 0% helix, 0% strand | Q90VG9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A, C
- GOL · Glycerol · additive · 8 copies · chains A, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.70 | 0.78 | 53 | empty |
| 2 | 589 | 0.69 | 0.78 | 57 | empty |
| 3 | 244 | 0.57 | 0.79 | 32 | EDO |
| 4 | 207 | 0.53 | 0.78 | 36 | empty |
| 5 | 196 | 0.51 | 0.77 | 39 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1343 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1306 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 989 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 984 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 374 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4U1K · HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential… · the same entry in another collection · chain F against F, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain E against A, TM-score 0.98
- 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 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 Q90VG9
- Elsewhere: RCSB PDB 4U1K · PDBe 4U1K · UniProt P01889 · UniProt P61769 · UniProt Q90VG9
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