MolNFT v1 · #53770 · protein
Crystal structure of MHC class I HLA-A2.1 bound to a peptide representing the epitope of the H5N1 (avian flu) nucleoprotein
2X4S · HLA class I histocompatibility antigen, a-2.1: “Crystal structure of MHC class I HLA-A2.1 bound to a peptide representing the epitope of the H5N1 (avian flu)…”. X-ray diffraction, 11 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 2X4S
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2.1; Beta-2-microglobulin; H5N1 influenza a…
- UniProt
- P01892, P61769
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a-2.1 | protein | 275 | 27% helix, 41% strand | P01892 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 51% strand | P61769 |
| C, F | H5N1 influenza a nucleoprotein | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B, D, E
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.77 | 0.80 | 93 | MES |
| 2 | 484 | 0.69 | 0.80 | 42 | GOL, MES |
| 3 | 130 | 0.46 | 0.78 | 25 | empty |
| 4 | 117 | 0.44 | 0.78 | 20 | empty |
| 5 | 52 | 0.44 | 0.84 | 17 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1401 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1379 Ų buried · 29 hydrogen bonds · protein-protein
- D–F · 846 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 841 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 530 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 modified (disulfide, engineered).
Compared structures
- 2X4S · Crystal structure of MHC CLass I HLA-A2.1 bound to a peptide representing the epitope of… · 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 E 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 2X4S · PDBe 2X4S · UniProt P01892 · UniProt P61769
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