Research workbench
DQ2-P.FLUOR-ALPHA1A
Analyse DQ2-P.FLUOR-ALPHA1A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U3M
- Type
- protein
- Length
- 746 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dq alpha 1 chain; MHC class II HLA-dq-beta-1…
- UniProt
- P01909, O19712
- Ligands
- NAG, PO4
- Pockets
- 7 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | HLA class II histocompatibility antigen, dq alpha 1 chain | protein | 181 | 14% helix, 44% strand | P01909 |
| D, B | MHC class II HLA-dq-beta-1 | protein | 181 | 20% helix, 45% strand | O19712 |
| E, F | ALPHA1A peptide | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains C, D, A
- PO4 · Phosphate ion · ion · chains D
- GOL · Glycerol · additive · 4 copies · chains C, D, F, A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.52 | 0.74 | 46 | GOL |
| 2 | 235 | 0.49 | 0.74 | 41 | GOL |
| 3 | 132 | 0.39 | 0.73 | 30 | empty |
| 4 | 137 | 0.39 | 0.73 | 32 | empty |
| 5 | 64 | 0.38 | 0.78 | 13 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2584 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2581 Ų buried · 51 hydrogen bonds · protein-protein
- D–F · 665 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 655 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 557 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
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 O19712
- Elsewhere: RCSB PDB 6U3M · PDBe 6U3M · UniProt P01909 · UniProt O19712
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