MolNFT v1 · #165697 · protein
LS2.8/3.15 - DQ2-P.FLUOR-ALPHA1A complex
6U3N · T-cell receptor, LS2.8/3.15 alpha: “LS2.8/3.15 - DQ2-P.FLUOR-ALPHA1A complex”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best druggability 0.72). MolNFT v1 #165697 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6U3N
- Type
- protein
- Length
- 814 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell receptor, LS2.8/3.15 alpha; T-cell receptor, LS2.8/3.15 beta; MHC class II…
- UniProt
- O19705, O19712
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | T-cell receptor, LS2.8/3.15 alpha | protein | 199 | 3% helix, 41% strand | — |
| E | T-cell receptor, LS2.8/3.15 beta | protein | 242 | 6% helix, 50% strand | — |
| A | MHC class II HLA-dq-alpha chain | protein | 181 | 14% helix, 40% strand | O19705 |
| B | MHC class II HLA-dq-beta-1 | protein | 181 | 19% helix, 40% strand | O19712 |
| C | Peptide | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.72 | 0.77 | 59 | empty |
| 2 | 50 | 0.71 | 0.98 | 19 | empty |
| 3 | 237 | 0.61 | 0.81 | 36 | empty |
| 4 | 179 | 0.47 | 0.76 | 30 | empty |
| 5 | 184 | 0.46 | 0.75 | 36 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2561 Ų buried · 52 hydrogen bonds · protein-protein
- D–E · 2101 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 655 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 583 Ų buried · 7 hydrogen bonds · protein-protein
- D–B · 395 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6U3N · LS2.8/3.15 - DQ2-P.fluor-alpha1a complex · the same entry in another collection · chain D against D, 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
- Every structure of UniProt O19705
- Every structure of UniProt O19712
- Elsewhere: RCSB PDB 6U3N · PDBe 6U3N · UniProt O19705 · UniProt O19712
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