Research workbench
Crystal structure of the mouse CD1D-lysosulfatide-HY19.3 TCR complex
Analyse Crystal structure of the mouse CD1D-lysosulfatide-HY19.3 TCR complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ELM
- Type
- protein
- Length
- 1,517 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2 microglobulin; HY19.3 TCR alpha chain…
- UniProt
- P11609, Q91XJ8
- Ligands
- SGF, PLM, NAG, BMA, FUC
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 11% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 266 | 25% helix, 40% strand | P11609 |
| C | Antigen-presenting glycoprotein CD1D1 | protein | 269 | 26% helix, 42% strand | P11609 |
| B | Beta-2 microglobulin | protein | 98 | 0% helix, 52% strand | Q91XJ8 |
| D | Beta-2 microglobulin | protein | 99 | 0% helix, 49% strand | Q91XJ8 |
| E | HY19.3 TCR alpha chain (mouse variable domain, human constant domain) | protein | 179 | 3% helix, 38% strand | — |
| F | HY19.3 TCR beta chain (mouse variable domain, human constant domain) | protein | 224 | 3% helix, 39% strand | — |
| G | HY19.3 TCR alpha chain (mouse variable domain, human constant domain) | protein | 171 | 2% helix, 40% strand | — |
| H | HY19.3 TCR beta chain (mouse variable domain, human constant domain) | protein | 211 | 7% helix, 38% strand | — |
Ligands and binding sites
- SGF · (2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl 3-O-sulfo-beta-D-galactopyranoside · ligand · 2 copies · chains A, H, C, F
- PLM · Palmitic acid · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, G, C, E
- BMA · beta-D-mannopyranose · sugar · chains E
- FUC · alpha-L-fucopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.87 | 0.90 | 60 | SGF, PLM |
| 2 | 746 | 0.84 | 0.87 | 78 | SGF, PLM |
| 3 | 701 | 0.76 | 0.81 | 79 | empty |
| 4 | 1172 | 0.74 | 0.77 | 135 | empty |
| 5 | 846 | 0.73 | 0.77 | 81 | empty |
Interfaces
11 interfaces between chains.
- E–F · 1439 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1381 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1214 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1205 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 585 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4ELM · Crystal structure of the mouse CD1d-lysosulfatide-Hy19.3 TCR complex · the same entry in another collection · chain H against H, TM-score 1.00
- P11609 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D1 (P11609) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P11609
- Every structure of UniProt Q91XJ8
- Elsewhere: RCSB PDB 4ELM · PDBe 4ELM · UniProt P11609 · UniProt Q91XJ8
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