Research workbench
Crystal structure of a autoimmune TCR-MHC complex
Analyse Crystal structure of a autoimmune TCR-MHC complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GRL
- 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 antigen; TCR HY.1B11 alpha chain; TCR…
- UniProt
- Q30066, Q67AJ6
- Ligands
- NAG
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class II HLA-dq-alpha chain | protein | 182 | 13% helix, 43% strand | Q30066 |
| B | MHC class II antigen | protein | 181 | 21% helix, 45% strand | Q67AJ6 |
| C | TCR HY.1B11 alpha chain | protein | 191 | 3% helix, 48% strand | — |
| D | TCR HY.1B11 beta chain | protein | 257 | 6% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.72 | 0.86 | 41 | empty |
| 2 | 1057 | 0.72 | 0.76 | 77 | empty |
| 3 | 140 | 0.48 | 0.78 | 23 | empty |
| 4 | 172 | 0.46 | 0.76 | 21 | empty |
| 5 | 100 | 0.37 | 0.75 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2743 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2290 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 960 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 716 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 175 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4GRL · Crystal structure of a autoimmune TCR-MHC complex · 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
- Elsewhere: RCSB PDB 4GRL · PDBe 4GRL · UniProt Q30066 · UniProt Q67AJ6
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