Research workbench
Crystal structure of F24 TCR -DR15-RQ13 peptide complex
Analyse Crystal structure of F24 TCR -DR15-RQ13 peptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CQQ
- Type
- protein
- Length
- 1,647 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; HLA-DRB1 protein; Peptide from…
- UniProt
- P01903, D7RIH9, P04591
- Ligands
- NAG, MG, SO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | HLA class II histocompatibility antigen, dr alpha chain | protein | 178 | 15% helix, 46% strand | P01903 |
| B | HLA-DRB1 protein | protein | 188 | 17% helix, 45% strand | D7RIH9 |
| C, H | Peptide from capsid protein P24 | protein | 13 | 0% helix, 15% strand | P04591 |
| D, I | F24 alpha chain | protein | 200 | 4% helix, 46% strand | — |
| E, J | F24 beta chain | protein | 244 | 9% helix, 49% strand | — |
| G | HLA-DRB1 protein | protein | 189 | 17% helix, 45% strand | D7RIH9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, F, G
- MG · Magnesium ion · metal · 2 copies · chains B, C, D
- SO4 · Sulfate ion · ion · chains D, E
- EDO · 1,2-ethanediol · additive · chains J
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 | 205 | 0.72 | 0.88 | 37 | empty |
| 2 | 985 | 0.70 | 0.75 | 81 | empty |
| 3 | 933 | 0.70 | 0.75 | 67 | empty |
| 4 | 472 | 0.69 | 0.80 | 43 | empty |
| 5 | 299 | 0.67 | 0.82 | 43 | MG |
Interfaces
23 interfaces between chains.
- F–G · 2517 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2492 Ų buried · 42 hydrogen bonds · protein-protein
- I–J · 2304 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 2300 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 737 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6CQQ · Crystal structure of F24 TCR -DR15-RQ13 peptide complex · the same entry in another collection · chain J against J, 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 0.97
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 D7RIH9
- Every structure of UniProt P04591
- Elsewhere: RCSB PDB 6CQQ · PDBe 6CQQ · UniProt P01903 · UniProt D7RIH9 · UniProt P04591
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