Research workbench
Crystal structure of MHC class I HLA-A2.1 bound to a photocleavable peptide
Analyse Crystal structure of MHC class I HLA-A2.1 bound to a photocleavable peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X4P
- Type
- protein
- Length
- 766 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; HLA-A2.1-restricted…
- UniProt
- P01892, P61769
- Ligands
- PRQ
- Pockets
- 6 · best druggability 0.75
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-2.1 | protein | 275 | 27% helix, 39% strand | P01892 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | HLA-A2.1-restricted influenza a matrix epitope | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- PRQ · (3S)-3-amino-3-(2-nitrophenyl)propanoic acid · ligand · 2 copies · chains A, C, D, F
- GOL · Glycerol · additive · 6 copies · chains A, B, D, E
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 5 copies · chains A, B, D, E
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 | 894 | 0.75 | 0.79 | 87 | GOL, MES |
| 2 | 561 | 0.67 | 0.77 | 55 | GOL, MES |
| 3 | 194 | 0.55 | 0.79 | 38 | GOL |
| 4 | 119 | 0.47 | 0.79 | 30 | empty |
| 5 | 121 | 0.45 | 0.78 | 21 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1429 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1364 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 816 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 801 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 334 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 covalent, 4 modified (disulfide, covalent ligand, engineered, nonstandard).
Compared structures
- 2X4P · Crystal structure of MHC CLass I HLA-A2.1 bound to a photocleavable peptide · the same entry in another collection · chain C against C, 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 2X4P · PDBe 2X4P · UniProt P01892 · UniProt P61769
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