Research workbench
Crystal structure of MHC class I HLA-A2.1 bound to cytomegalovirus (CMV) PP65 epitope
Analyse Crystal structure of MHC class I HLA-A2.1 bound to cytomegalovirus (CMV) PP65… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X4R
- 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; 65 kda phosphoprotein
- UniProt
- P01892, P61769, P06725
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class I histocompatibility antigen, a-2.1 | protein | 275 | 28% helix, 39% strand | P01892 |
| B, E | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | 65 kda phosphoprotein | protein | 9 | 0% helix, 0% strand | P06725 |
Ligands and binding sites
- GOL · Glycerol · additive · 9 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.76 | 0.78 | 92 | GOL |
| 2 | 575 | 0.67 | 0.77 | 53 | GOL |
| 3 | 55 | 0.59 | 0.91 | 15 | GOL |
| 4 | 61 | 0.53 | 0.86 | 16 | GOL |
| 5 | 79 | 0.51 | 0.84 | 23 | GOL |
Interfaces
5 interfaces between chains.
- D–E · 1390 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1365 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 797 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 786 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 486 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2X4R · Crystal structure of MHC CLass I HLA-A2.1 bound to Cytomegalovirus (CMV) pp65 epitope · 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
- Every structure of UniProt P06725
- Elsewhere: RCSB PDB 2X4R · PDBe 2X4R · UniProt P01892 · UniProt P61769 · UniProt P06725
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