Research workbench
Crystal structure of F5 TCR -DR11-RQ13 peptide complex
Analyse Crystal structure of F5 TCR -DR11-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
- 6CQN
- Type
- protein
- Length
- 825 residues
- Chains
- 5
- 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, MG, SO4, CL
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 178 | 14% helix, 46% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-11 beta chain | protein | 190 | 17% helix, 44% strand | P20039 |
| C | Peptide from capsid protein P24 | protein | 13 | 0% helix, 15% strand | P04591 |
| D | F5 alpha chain | protein | 200 | 4% helix, 44% strand | — |
| E | F5 beta chain | protein | 244 | 7% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, E
- CL · Chloride ion · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.73 | 0.76 | 80 | empty |
| 2 | 294 | 0.64 | 0.81 | 41 | MG, CL |
| 3 | 146 | 0.49 | 0.78 | 20 | empty |
| 4 | 163 | 0.46 | 0.76 | 27 | empty |
| 5 | 148 | 0.43 | 0.74 | 24 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2411 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 2272 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 692 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 687 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 274 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6CQN · Crystal structure of F5 TCR -DR11-RQ13 peptide complex · the same entry in another collection · chain A against A, 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 P20039
- Every structure of UniProt P04591
- Elsewhere: RCSB PDB 6CQN · PDBe 6CQN · UniProt P01903 · UniProt P20039 · UniProt P04591
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