Research workbench
W316 TCR in complex with HLA-DQ2-OMEGA1
Analyse W316 TCR in complex with HLA-DQ2-OMEGA1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SG0
- Type
- protein
- Length
- 805 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dq alpha 1 chain; MHC class II HLA-dq-beta-1…
- UniProt
- P01909, O19712
- Ligands
- NAG
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dq alpha 1 chain | protein | 180 | 14% helix, 44% strand | P01909 |
| B | MHC class II HLA-dq-beta-1 | protein | 175 | 18% helix, 43% strand | O19712 |
| C | DQ2-glia-OMEGA1 peptide | protein | 11 | 0% helix, 0% strand | — |
| D | T-cell receptor, W316, alpha chain | protein | 201 | 1% helix, 42% strand | — |
| E | T-cell receptor, W316, beta chain | protein | 238 | 8% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, D, E
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 | 842 | 0.71 | 0.77 | 76 | empty |
| 2 | 409 | 0.71 | 0.82 | 53 | empty |
| 3 | 106 | 0.66 | 0.90 | 24 | empty |
| 4 | 198 | 0.48 | 0.75 | 41 | empty |
| 5 | 166 | 0.46 | 0.75 | 28 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2609 Ų buried · 47 hydrogen bonds · protein-protein
- D–E · 2011 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 667 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 549 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 316 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 P01909
- Every structure of UniProt O19712
- Elsewhere: RCSB PDB 7SG0 · PDBe 7SG0 · UniProt P01909 · UniProt O19712
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