MolNFT v1 · #107323 · protein
Crystal structure of HLA-A*0201 in complex with alqda, a 15 mer self- peptide
4U6X · HLA class I histocompatibility antigen, a-2 alpha chain: “Crystal structure of HLA-A*0201 in complex with alqda, a 15 mer self- peptide”. X-ray diffraction, 2 ligands (MG, CL), 3 pockets (best druggability 0.68). MolNFT v1 #107323…
- PDB
- 4U6X
- Type
- protein
- Length
- 384 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; Alqda…
- UniProt
- P01892, P61769
- Ligands
- MG, CL
- Pockets
- 3 · best druggability 0.68
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, a-2 alpha chain | protein | 274 | 27% helix, 40% strand | P01892 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| P | Alqda peptide, alqdagdssrkeyfi | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, A, P
- CL · Chloride ion · ion · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.68 | 0.77 | 57 | PEG, CL |
| 2 | 156 | 0.48 | 0.77 | 28 | empty |
| 3 | 65 | 0.33 | 0.76 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1378 Ų buried · 25 hydrogen bonds · protein-protein
- A–P · 878 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4U6X · Crystal Structure of HLA-A*0201 in complex with ALQDA, a 15 mer self-peptide · 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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 4U6X · PDBe 4U6X · UniProt P01892 · UniProt P61769
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