MolNFT v1 · #53765 · protein
Crystal structure of MHC class I HLA-A2.1 bound to residual fragments of a photocleavable peptide that is cleaved upon UV-light treatment
2X4N · HLA class I histocompatibility antigen, a-2 alpha chain: “Crystal structure of MHC class I HLA-A2.1 bound to residual fragments of a photocleavable peptide that is…”. X-ray diffraction, 1 ligand (PRV), 11 pockets (best druggability…
- PDB
- 2X4N
- Type
- protein
- Length
- 760 residues
- Chains
- 6
- 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…
- UniProt
- P01892, P61769
- Ligands
- PRV
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 275 | 27% helix, 39% strand | P01892 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 45% strand | P61769 |
| C, F | HLA-A2.1-restricted influenza a matrix epitope | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- PRV · (2R)-amino(2-nitrophenyl)ethanoic acid · ion · 2 copies · chains C, F
- GOL · Glycerol · additive · 10 copies · chains A, B, D, E
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.73 | 0.76 | 98 | GOL, MES |
| 2 | 596 | 0.68 | 0.77 | 63 | GOL |
| 3 | 137 | 0.54 | 0.81 | 30 | GOL |
| 4 | 149 | 0.53 | 0.80 | 28 | GOL |
| 5 | 191 | 0.49 | 0.76 | 30 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1399 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1358 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 628 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 618 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 316 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2X4N · Crystal structure of MHC CLass I HLA-A2.1 bound to residual fragments of a photocleavable… · 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 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 2X4N · PDBe 2X4N · UniProt P01892 · UniProt P61769
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.