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Crystal structure of human class I MHC (HLA-A2.1) complexed with beta 2-microglobulin and HIV-rt variant peptide I1Y
Analyse Crystal structure of human class I MHC (HLA-A2.1) complexed with beta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I1F
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (class I histocompatibility antigen, gogo-A0201 alpha chain); Protein (beta…
- UniProt
- P01892, P61769
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Protein (class I histocompatibility antigen, gogo-A0201 alpha chain) | protein | 275 | 27% helix, 40% strand | P01892 |
| B, E | Protein (beta 2-microglobulin) | protein | 100 | 0% helix, 49% strand | P61769 |
| C, F | Protein (HIV-rt variant peptide I1F (flkepvhgv)) | protein | 9 | 0% helix, 0% strand | — |
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 | 719 | 0.70 | 0.77 | 60 | empty |
| 2 | 683 | 0.69 | 0.77 | 53 | empty |
| 3 | 184 | 0.50 | 0.77 | 30 | empty |
| 4 | 119 | 0.45 | 0.78 | 19 | empty |
| 5 | 69 | 0.35 | 0.77 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1432 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 1410 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 846 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 842 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1I1F · Crystal structure of human class i mhc (hla-a2.1) complexed with beta 2-microglobulin and… · 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 1I1F · PDBe 1I1F · UniProt P01892 · UniProt P61769
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