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
- 4U1M
- Type
- protein
- Length
- 386 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, B-42 alpha chain; Beta-2-microglobulin; Protein…
- UniProt
- P30480, P61769, Q90VG9
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-42 alpha chain | protein | 277 | 27% helix, 39% strand | P30480 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Protein nef | protein | 9 | 0% helix, 0% strand | Q90VG9 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 26 copies · chains A, C, B
- GOL · Glycerol · additive · 4 copies · chains A, C, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.71 | 0.98 | 21 | EDO, GOL |
| 2 | 683 | 0.69 | 0.77 | 60 | GOL, EDO |
| 3 | 131 | 0.49 | 0.80 | 26 | EDO |
| 4 | 62 | 0.39 | 0.80 | 15 | EDO |
| 5 | 71 | 0.38 | 0.78 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1322 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 933 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4U1M · 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
- 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 P30480
- Every structure of UniProt P61769
- Every structure of UniProt Q90VG9
- Elsewhere: RCSB PDB 4U1M · PDBe 4U1M · UniProt P30480 · UniProt P61769 · UniProt Q90VG9
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