Research workbench
Crystal structure of DR1 presenting the RQ13 peptide
Analyse Crystal structure of DR1 presenting the RQ13 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CQJ
- Type
- protein
- Length
- 1,125 residues
- Chains
- 9
- 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, P04229, P04591
- Ligands
- NAG, NA
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | HLA class II histocompatibility antigen, dr alpha chain | protein | 180 | 15% helix, 46% strand | P01903 |
| B, H | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 182 | 18% helix, 46% strand | P04229 |
| C, F, I | Peptide from capsid protein P24 | protein | 13 | 0% helix, 8% strand | P04591 |
| D | HLA class II histocompatibility antigen, dr alpha chain | protein | 182 | 15% helix, 46% strand | P01903 |
| E | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 180 | 18% helix, 47% strand | P04229 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains G, H, A, B, D
- NA · Sodium ion · metal · 2 copies · chains D, G
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.73 | 0.78 | 62 | empty |
| 2 | 799 | 0.73 | 0.78 | 62 | empty |
| 3 | 187 | 0.45 | 0.75 | 30 | empty |
| 4 | 177 | 0.44 | 0.73 | 26 | empty |
| 5 | 162 | 0.40 | 0.73 | 21 | empty |
Interfaces
18 interfaces between chains.
- G–H · 2592 Ų buried · 49 hydrogen bonds · protein-protein
- D–E · 2592 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2552 Ų buried · 45 hydrogen bonds · protein-protein
- H–I · 737 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 736 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6CQJ · Crystal structure of DR1 presenting the RQ13 peptide · the same entry in another collection · chain I against I, 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 G 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 P04229
- Every structure of UniProt P04591
- Elsewhere: RCSB PDB 6CQJ · PDBe 6CQJ · UniProt P01903 · UniProt P04229 · UniProt P04591
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