Research workbench
The structure of HLA-dra, DRB3*0101 (DR52A) with bound platelet integrin peptide associated with fetal and neonatal alloimmune thrombocytopenia
Analyse The structure of HLA-dra, DRB3*0101 (DR52A) with bound platelet integrin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q6W
- Type
- protein
- Length
- 758 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, P79483, P05106
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 14% helix, 47% strand | P01903 |
| B, E | HLA class II histocompatibility antigen, DRB3-1 beta chain | protein | 188 | 14% helix, 45% strand | P79483 |
| C | Integrin beta-3 | protein | 11 | 0% helix, 9% strand | P05106 |
| D | HLA class II histocompatibility antigen, dr alpha chain | protein | 180 | 13% helix, 48% strand | P01903 |
| F | Integrin beta-3 | protein | 12 | 0% helix, 8% strand | P05106 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.74 | 0.80 | 83 | empty |
| 2 | 285 | 0.62 | 0.79 | 39 | empty |
| 3 | 254 | 0.58 | 0.79 | 34 | empty |
| 4 | 95 | 0.46 | 0.80 | 26 | empty |
| 5 | 64 | 0.28 | 0.73 | 17 | empty |
Interfaces
10 interfaces between chains.
- D–E · 2532 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2413 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 676 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 654 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 562 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2Q6W · The structure of HLA-DRA, DRB3*0101 (DR52a) with bound platelet integrin peptide… · the same entry in another collection · chain F against F, TM-score 1.00
- P79483 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr beta 3… · a predicted model of the same protein · chain E against A, TM-score 0.98
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · 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 P01903
- Every structure of UniProt P79483
- Every structure of UniProt P05106
- Elsewhere: RCSB PDB 2Q6W · PDBe 2Q6W · UniProt P01903 · UniProt P79483 · UniProt P05106
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