Research workbench
Structural and functional studies of the trans-encoded HLA-DQ2.3 (DQA1*03:01/DQB1*02:01) molecule
Analyse Structural and functional studies of the trans-encoded HLA-DQ2.3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D8P
- Type
- protein
- Length
- 753 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA-DQA1 protein; Peptide from gamma-GLIADIN,HLA class II histocompatibility antigen, dq…
- UniProt
- L8E864, Q94G94, Q5Y7D3
- Pockets
- 7 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA-DQA1 protein | protein | 184 | 11% helix, 43% strand | L8E864 |
| B, D | Peptide from gamma-GLIADIN,HLA class II histocompatibility antigen, dq beta 1 chain | protein | 193 | 18% helix, 40% strand | Q94G94, Q5Y7D3 |
| C | HLA-DQA1 protein | protein | 183 | 11% helix, 43% strand | L8E864 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.57 | 0.75 | 52 | GOL |
| 2 | 271 | 0.52 | 0.75 | 41 | empty |
| 3 | 199 | 0.48 | 0.75 | 29 | empty |
| 4 | 186 | 0.47 | 0.75 | 22 | empty |
| 5 | 184 | 0.45 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3157 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 3081 Ų buried · 59 hydrogen bonds · protein-protein
- B–D · 716 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4D8P · Structural and functional studies of the trans-encoded HLA-DQ2.3 (DQA1*03:01/DQB1*02:01)… · the same entry in another collection · chain A against A, TM-score 1.00
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 L8E864
- Every structure of UniProt Q94G94
- Every structure of UniProt Q5Y7D3
- Elsewhere: RCSB PDB 4D8P · PDBe 4D8P · UniProt L8E864 · UniProt Q94G94 · UniProt Q5Y7D3
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