Research workbench
HLA class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope
Analyse HLA class II peptide flanking residues tune the immunogenicity of a human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HBY
- Type
- protein
- Length
- 777 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
- UniProt
- P01903, P04229
- Ligands
- PO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 178 | 15% helix, 47% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 191 | 19% helix, 45% strand | P04229 |
| C, F | Arrpplaelaalnlsgsrl 5T4 tumour epitope | protein | 19 | 0% helix, 5% strand | — |
| D | HLA class II histocompatibility antigen, dr alpha chain | protein | 180 | 14% helix, 46% strand | P01903 |
| E | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 190 | 19% helix, 45% strand | P04229 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains A, E, B, D
- EDO · 1,2-ethanediol · additive · 25 copies · chains A, B, C, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.78 | 0.80 | 73 | EDO |
| 2 | 1161 | 0.77 | 0.80 | 96 | EDO, PO4 |
| 3 | 131 | 0.46 | 0.77 | 22 | empty |
| 4 | 126 | 0.40 | 0.75 | 24 | empty |
| 5 | 78 | 0.33 | 0.75 | 18 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2647 Ų buried · 45 hydrogen bonds · protein-protein
- D–E · 2546 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 724 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 720 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 683 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6HBY · HLA class II peptide flanking residues tune the immunogenicity of a human tumor-derived… · the same entry in another collection · chain F against F, TM-score 1.00
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P01903
- Every structure of UniProt P04229
- Elsewhere: RCSB PDB 6HBY · PDBe 6HBY · UniProt P01903 · UniProt P04229
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