MolNFT v1 · #107324 · protein
Crystal structure of HLA-A*0201 in complex with flndk, a 15 mer self- peptide
4U6Y · HLA class I histocompatibility antigen, a-2 alpha chain: “Crystal structure of HLA-A*0201 in complex with flndk, a 15 mer self- peptide”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.70). MolNFT v1 #107324 on…
- PDB
- 4U6Y
- 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, a-2 alpha chain; Beta-2-microglobulin; Flnkd…
- UniProt
- P01892, P61769
- Ligands
- CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% 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 | 97 | 0% helix, 51% strand | P61769 |
| P | Flnkd peptide, flnkdlevdghfvtm | protein | 15 | 0% helix, 27% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.70 | 0.78 | 59 | empty |
| 2 | 163 | 0.48 | 0.77 | 25 | empty |
| 3 | 87 | 0.45 | 0.81 | 19 | empty |
| 4 | 57 | 0.31 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1168 Ų buried · 16 hydrogen bonds · protein-protein
- A–P · 1004 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4U6Y · Crystal Structure of HLA-A*0201 in complex with FLNDK, 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 0.98
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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 4U6Y · PDBe 4U6Y · UniProt P01892 · UniProt P61769
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