Research workbench
F11 T-cell receptor recognising pkyvkqntlklat peptide presented by HLA-DR*0101
Analyse F11 T-cell receptor recognising pkyvkqntlklat peptide presented by HLA-DR*0101 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FUP
- Type
- protein
- Length
- 442 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human F11 T-cell receptor alpha chain; Human F11 T-cell receptor beta chain
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human F11 T-cell receptor alpha chain | protein | 202 | 8% helix, 45% strand | — |
| B | Human F11 T-cell receptor beta chain | protein | 240 | 7% helix, 54% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 25 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.73 | 0.76 | 81 | EDO, PEG |
| 2 | 125 | 0.42 | 0.76 | 25 | EDO |
| 3 | 100 | 0.39 | 0.76 | 23 | PEG |
| 4 | 57 | 0.35 | 0.78 | 17 | EDO |
| 5 | 58 | 0.32 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2135 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6FUP · F11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented by HLA-DR*0101 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6FUP · PDBe 6FUP
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