Research workbench
3C11-DQ2-glia-A2 complex
Analyse 3C11-DQ2-glia-A2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XP6
- Type
- protein
- Length
- 1,607 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II HLA-dq-alpha chain; MHC class II HLA-dq-beta-1; 3.C11 igh Fab; 3.C11 igk…
- UniProt
- O19705, O19712
- Ligands
- NAG, BMA, FUC, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 8 distinct chains · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class II HLA-dq-alpha chain | protein | 181 | 14% helix, 44% strand | O19705 |
| B | MHC class II HLA-dq-beta-1 | protein | 181 | 20% helix, 46% strand | O19712 |
| D | MHC class II HLA-dq-alpha chain | protein | 182 | 14% helix, 44% strand | O19705 |
| E | MHC class II HLA-dq-beta-1 | protein | 180 | 21% helix, 45% strand | O19712 |
| H | 3.C11 igh Fab | protein | 220 | 10% helix, 51% strand | — |
| J | 3.C11 igh Fab | protein | 213 | 10% helix, 51% strand | — |
| G, I | 3.C11 igk Fab | protein | 212 | 6% helix, 51% strand | — |
| C, F | DQ2-glia-A2 peptide | protein | 13 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, D, E
- BMA · beta-D-mannopyranose · sugar · 5 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B
- CL · Chloride ion · ion · 4 copies · chains H, J, G
- IPA · Isopropyl alcohol · additive · 12 copies · chains A, B, E, D, H, G, C, J, I, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.77 | 0.97 | 18 | empty |
| 2 | 903 | 0.70 | 0.75 | 57 | IPA |
| 3 | 812 | 0.67 | 0.74 | 58 | IPA |
| 4 | 622 | 0.63 | 0.74 | 52 | empty |
| 5 | 396 | 0.57 | 0.74 | 45 | empty |
Interfaces
23 interfaces between chains.
- A–B · 2625 Ų buried · 48 hydrogen bonds · protein-protein
- D–E · 2622 Ų buried · 43 hydrogen bonds · protein-protein
- H–G · 1911 Ų buried · 11 hydrogen bonds · protein-protein
- J–I · 1769 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 723 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6XP6 · 3C11-DQ2-glia-a2 complex · 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 O19705
- Every structure of UniProt O19712
- Elsewhere: RCSB PDB 6XP6 · PDBe 6XP6 · UniProt O19705 · UniProt O19712
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