Research workbench
Crystal structure of F24 TCR -DR1-RQ13 peptide complex
Analyse Crystal structure of F24 TCR -DR1-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
- 6CQR
- Type
- protein
- Length
- 1,655 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 class II histocompatibility…
- UniProt
- P01903, P04229, P04591
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 14% helix, 46% strand | P01903 |
| B, G | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 190 | 16% helix, 44% strand | P04229 |
| C, H | Peptide from capsid protein P24 | protein | 13 | 0% helix, 15% strand | P04591 |
| D | F24 alpha chain | protein | 200 | 3% helix, 45% strand | — |
| E, J | F24 beta chain | protein | 245 | 7% helix, 49% strand | — |
| I | F24 alpha chain | protein | 201 | 4% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B, J, F, G
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 | 1019 | 0.76 | 0.78 | 78 | empty |
| 2 | 803 | 0.75 | 0.79 | 70 | empty |
| 3 | 947 | 0.74 | 0.78 | 74 | empty |
| 4 | 303 | 0.71 | 0.84 | 41 | empty |
| 5 | 355 | 0.69 | 0.82 | 46 | empty |
Interfaces
24 interfaces between chains.
- F–G · 2567 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2551 Ų buried · 45 hydrogen bonds · protein-protein
- I–J · 2318 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 2312 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 712 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6CQR · Crystal structure of F24 TCR -DR1-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 F 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 P04229
- Every structure of UniProt P04591
- Elsewhere: RCSB PDB 6CQR · PDBe 6CQR · UniProt P01903 · UniProt P04229 · UniProt P04591
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