Research workbench
JR51 DQ2-P.AERU-ALPHA2A complex
Analyse JR51 DQ2-P.AERU-ALPHA2A complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U3O
- Type
- protein
- Length
- 1,622 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell receptor, JR5.1 alpha; T-cell receptor, JR5.1 beta; MHC class II HLA-dq-alpha…
- UniProt
- O19705, O19712
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, A | T-cell receptor, JR5.1 alpha | protein | 194 | 3% helix, 42% strand | — |
| H, B | T-cell receptor, JR5.1 beta | protein | 242 | 6% helix, 50% strand | — |
| C, E | MHC class II HLA-dq-alpha chain | protein | 181 | 14% helix, 44% strand | O19705 |
| D, F | MHC class II HLA-dq-beta-1 | protein | 181 | 20% helix, 45% strand | O19712 |
| I, J | Peptide | protein | 13 | 0% helix, 8% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.73 | 0.77 | 97 | empty |
| 2 | 845 | 0.72 | 0.77 | 89 | empty |
| 3 | 264 | 0.62 | 0.81 | 41 | empty |
| 4 | 113 | 0.58 | 0.85 | 31 | empty |
| 5 | 88 | 0.58 | 0.87 | 27 | empty |
Interfaces
21 interfaces between chains.
- C–D · 2621 Ų buried · 52 hydrogen bonds · protein-protein
- E–F · 2593 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 2171 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 2144 Ų buried · 25 hydrogen bonds · protein-protein
- G–A · 798 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6U3O · JR51 DQ2-p.aeru-alpha2a complex · the same entry in another collection · chain G against G, 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 O19705
- Every structure of UniProt O19712
- Elsewhere: RCSB PDB 6U3O · PDBe 6U3O · UniProt O19705 · UniProt O19712
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