Research workbench
Structure of HLA-A2:01 with peptide MM91
Analyse Structure of HLA-A2:01 with peptide MM91 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O4Y
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Peptide MM91
- UniProt
- U5YJM1, P61769
- Ligands
- NA
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 274 | 27% helix, 41% strand | U5YJM1 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Peptide MM91 | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.66 | 0.78 | 46 | GOL |
| 2 | 55 | 0.46 | 0.84 | 16 | GOL |
| 3 | 79 | 0.43 | 0.80 | 16 | empty |
| 4 | 90 | 0.34 | 0.75 | 20 | empty |
| 5 | 58 | 0.31 | 0.76 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1304 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 793 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
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 U5YJM1
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6O4Y · PDBe 6O4Y · UniProt U5YJM1 · UniProt P61769
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.