Research workbench
Crystal structure of DR11 presenting the GAG293 epitope
Analyse Crystal structure of DR11 presenting the GAG293 epitope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CPL
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- 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, P20039, P04591
- Ligands
- NAG, NA, SO4
- Pockets
- 3 · best druggability 0.39
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 180 | 14% helix, 46% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-11 beta chain | protein | 189 | 17% helix, 46% strand | P20039 |
| C | Gag polyprotein | protein | 16 | 0% helix, 6% strand | P04591 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.39 | 0.73 | 20 | empty |
| 2 | 117 | 0.38 | 0.74 | 18 | empty |
| 3 | 82 | 0.30 | 0.73 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2630 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 714 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 691 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6CPL · Crystal structure of DR11 presenting the gag293 epitope · the same entry in another collection · chain C against C, TM-score 1.00
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P20039
- Every structure of UniProt P04591
- Elsewhere: RCSB PDB 6CPL · PDBe 6CPL · UniProt P01903 · UniProt P20039 · UniProt P04591
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