MolNFT v1 · #75266 · protein
Structure of autoimmune TCR HY.1B11 in complex with HLA-DQ1 and mbp 85-99
3PL6 · MHC class II HLA-dq-alpha chain: “Structure of autoimmune TCR HY.1B11 in complex with HLA-DQ1 and mbp 85-99”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability 0.73). MolNFT v1 #75266 on GenesisL1: 3D structure…
- PDB
- 3PL6
- Type
- protein
- Length
- 811 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II HLA-dq-alpha chain; MHC class II HLA-dq-beta chain; T-cell receptor alpha…
- UniProt
- Q30066, Q67AJ6, D3YTB3
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class II HLA-dq-alpha chain | protein | 182 | 11% helix, 44% strand | Q30066 |
| B | MHC class II HLA-dq-beta chain | protein | 181 | 21% helix, 46% strand | Q67AJ6 |
| C | T-cell receptor alpha chain | protein | 191 | 2% helix, 47% strand | — |
| D | Mbp peptide / T-cell receptor beta chain chimera | protein | 257 | 7% helix, 46% strand | D3YTB3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.73 | 0.84 | 49 | empty |
| 2 | 983 | 0.72 | 0.76 | 73 | empty |
| 3 | 92 | 0.51 | 0.83 | 25 | empty |
| 4 | 224 | 0.51 | 0.76 | 41 | empty |
| 5 | 144 | 0.49 | 0.79 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2722 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2289 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 945 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 803 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 164 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3PL6 · Structure of Autoimmune TCR Hy.1B11 in complex with HLA-DQ1 and MBP 85-99 · 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
- Every structure of UniProt Q30066
- Every structure of UniProt Q67AJ6
- Every structure of UniProt D3YTB3
- Elsewhere: RCSB PDB 3PL6 · PDBe 3PL6 · UniProt Q30066 · UniProt Q67AJ6 · UniProt D3YTB3
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