MolNFT v1 · #145522 · protein
Crystal structure of F24 TCR -DR11-RQ13 peptide complex
6CQL · HLA class II histocompatibility antigen, dr alpha chain: “Crystal structure of F24 TCR -DR11-RQ13 peptide complex”. X-ray diffraction, 2 ligands (NAG, MG), 10 pockets (best druggability 0.73). MolNFT v1 #145522 on GenesisL1: 3D…
- PDB
- 6CQL
- 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
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 178 | 14% helix, 47% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-11 beta chain | protein | 190 | 19% helix, 44% strand | P20039 |
| C | Peptide from capsid protein P24 | protein | 13 | 0% helix, 15% strand | P04591 |
| D | F24 alpha chain | protein | 200 | 5% helix, 45% strand | — |
| E | F24 beta chain | protein | 244 | 7% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.73 | 0.77 | 82 | empty |
| 2 | 278 | 0.67 | 0.83 | 39 | empty |
| 3 | 170 | 0.48 | 0.77 | 20 | empty |
| 4 | 149 | 0.47 | 0.77 | 18 | empty |
| 5 | 163 | 0.44 | 0.75 | 27 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2477 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2195 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 696 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 684 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 276 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6CQL · Crystal structure of F24 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 6CQL · PDBe 6CQL · UniProt P01903 · UniProt P20039 · UniProt P04591
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