Research workbench
Crystal structure of LS10-TCR/M1-HLA-A*02 complex
Analyse Crystal structure of LS10-TCR/M1-HLA-A*02 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JHD
- Type
- protein
- Length
- 1,652 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-2 alpha chain; Beta-2-microglobulin; Influenza…
- UniProt
- P01892, P61769
- Ligands
- EDT
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | HLA class I histocompatibility antigen, a-2 alpha chain | protein | 276 | 26% helix, 41% strand | P01892 |
| B, G | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C, H | Influenza M1(58-66) peptide | protein | 9 | 0% helix, 0% strand | — |
| D | Tcralpha chain | protein | 201 | 3% helix, 42% strand | — |
| E, J | Tcrbeta chain | protein | 239 | 6% helix, 49% strand | — |
| I | Tcralpha chain | protein | 203 | 1% helix, 43% strand | — |
Ligands and binding sites
- EDT · {[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid · ligand · 2 copies · chains E, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.76 | 0.79 | 62 | empty |
| 2 | 1017 | 0.73 | 0.77 | 107 | EDT |
| 3 | 1017 | 0.71 | 0.75 | 94 | empty |
| 4 | 965 | 0.71 | 0.75 | 74 | empty |
| 5 | 594 | 0.69 | 0.78 | 54 | empty |
Interfaces
18 interfaces between chains.
- D–E · 2208 Ų buried · 24 hydrogen bonds · protein-protein
- I–J · 2152 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1482 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1480 Ų buried · 20 hydrogen bonds · protein-protein
- F–H · 831 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 1 covalent (disulfide, covalent ligand).
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 P01892
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5JHD · PDBe 5JHD · UniProt P01892 · UniProt P61769
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