Research workbench
Structure of the MHC class II molecule HLA-DQ8 bound with a deamidated gluten peptide
Analyse Structure of the MHC class II molecule HLA-DQ8 bound with a deamidated gluten… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NNA
- Type
- protein
- Length
- 377 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II antigen; Gluten peptide
- UniProt
- Q5Y7F5, Q5Y7F6, P18573
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class II antigen | protein | 182 | 15% helix, 45% strand | Q5Y7F5 |
| B | MHC class II antigen | protein | 182 | 20% helix, 42% strand | Q5Y7F6 |
| C | Gluten peptide | protein | 13 | 0% helix, 8% strand | P18573 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.47 | 0.74 | 27 | empty |
| 2 | 94 | 0.35 | 0.74 | 19 | empty |
| 3 | 50 | 0.26 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2673 Ų buried · 57 hydrogen bonds · protein-protein
- B–C · 721 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 647 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2NNA · Structure of the MHC class II molecule HLA-DQ8 bound with a deamidated gluten peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P18573 · AlphaFold monomer V2.0 prediction for ALPHA/BETA-gliadin MM1 (P18573) · a predicted model of the same protein · chain C against A, TM-score 0.43
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 Q5Y7F5
- Every structure of UniProt Q5Y7F6
- Every structure of UniProt P18573
- Elsewhere: RCSB PDB 2NNA · PDBe 2NNA · UniProt Q5Y7F5 · UniProt Q5Y7F6 · UniProt P18573
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