MolNFT v1 · #107164 · protein
HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes
4U1N · HLA class I histocompatibility antigen, B-42 alpha chain: “HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through…”. X-ray diffraction, 6 pockets (best druggability 0.72). MolNFT…
- PDB
- 4U1N
- Type
- protein
- Length
- 387 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
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, B-42 alpha chain | protein | 278 | 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 · 12 copies · chains A, C, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.72 | 0.98 | 21 | EDO |
| 2 | 675 | 0.69 | 0.77 | 57 | EDO, GOL |
| 3 | 157 | 0.53 | 0.80 | 30 | empty |
| 4 | 59 | 0.40 | 0.81 | 16 | EDO |
| 5 | 59 | 0.36 | 0.78 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1394 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 924 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4U1N · 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 0.99
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 4U1N · PDBe 4U1N · UniProt P30480 · UniProt P61769 · UniProt Q90VG9
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