Research workbench
Crystal structure of HLA-DQ2 complexed with deamidated gliadin peptide
Analyse Crystal structure of HLA-DQ2 complexed with deamidated gliadin peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S9V
- Type
- protein
- Length
- 739 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, DQ(3) alpha chain; HLA class II…
- UniProt
- P01909, P01918
- Pockets
- 9 · best druggability 0.48
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, DQ(3) alpha chain | protein | 179 | 15% helix, 44% strand | P01909 |
| B | HLA class II histocompatibility antigen, DQ(1) beta chain | protein | 181 | 20% helix, 45% strand | P01918 |
| C, F | Alpha-I gliadin | protein | 11 | 0% helix, 0% strand | — |
| D | HLA class II histocompatibility antigen, DQ(3) alpha chain | protein | 177 | 14% helix, 44% strand | P01909 |
| E | HLA class II histocompatibility antigen, DQ(1) beta chain | protein | 180 | 21% helix, 46% strand | P01918 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.48 | 0.75 | 36 | empty |
| 2 | 97 | 0.46 | 0.80 | 23 | empty |
| 3 | 167 | 0.43 | 0.75 | 32 | empty |
| 4 | 152 | 0.42 | 0.74 | 24 | empty |
| 5 | 122 | 0.40 | 0.75 | 21 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2523 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2522 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 615 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 556 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 539 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1S9V · Crystal structure of HLA-DQ2 complexed with deamidated gliadin peptide · the same entry in another collection · chain F against F, TM-score 1.00
- P01909 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dq alpha 1… · a predicted model of the same protein · chain D against A, TM-score 0.96
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 P01909
- Every structure of UniProt P01918
- Elsewhere: RCSB PDB 1S9V · PDBe 1S9V · UniProt P01909 · UniProt P01918
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