Research workbench
T316 complex
Analyse T316 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z7W
- Type
- protein
- Length
- 1,622 residues
- Chains
- 10
- 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-1; T-cell receptor, T316 alpha…
- UniProt
- Q30069, O19707
- Ligands
- NAG, MAN, FUC, SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 7 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | MHC class II HLA-dq-alpha chain | protein | 181 | 15% helix, 45% strand | Q30069 |
| B, D | MHC class II HLA-dq-beta-1 | protein | 180 | 18% helix, 44% strand | O19707 |
| E | T-cell receptor, T316 alpha chain | protein | 199 | 3% helix, 40% strand | — |
| F | T-cell receptor, T316 beta chain | protein | 241 | 6% helix, 49% strand | — |
| G | T-cell receptor, T316 alpha chain | protein | 191 | 3% helix, 42% strand | — |
| H | T-cell receptor, T316 beta chain | protein | 239 | 6% helix, 46% strand | — |
| I, J | DQ8-glia-ALPHA1 | protein | 15 | 0% helix, 7% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, F, C, H, J
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains F, D, H, B
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, F, I, J, C, H
- SO4 · Sulfate ion · ion · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.74 | 0.78 | 79 | empty |
| 2 | 972 | 0.72 | 0.76 | 86 | empty |
| 3 | 485 | 0.67 | 0.78 | 64 | MAN, FUC |
| 4 | 145 | 0.59 | 0.83 | 33 | MAN |
| 5 | 96 | 0.59 | 0.87 | 20 | empty |
Interfaces
25 interfaces between chains.
- C–D · 2611 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 2590 Ų buried · 58 hydrogen bonds · protein-protein
- E–F · 2264 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1728 Ų buried · 13 hydrogen bonds · protein-protein
- B–J · 729 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4Z7W · T316 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 Q30069
- Every structure of UniProt O19707
- Elsewhere: RCSB PDB 4Z7W · PDBe 4Z7W · UniProt Q30069 · UniProt O19707
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