Research workbench
Crystal structure of the MCD1D/EF77/INKTCR ternary complex
Analyse Crystal structure of the MCD1D/EF77/INKTCR ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y4K
- Type
- protein
- Length
- 805 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; Chimeric TCR…
- UniProt
- P11609, P01887
- Ligands
- 49Y, NAG, FUC
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 268 | 26% helix, 40% strand | P11609 |
| B | Beta-2-microglobulin | protein | 96 | 0% helix, 51% strand | P01887 |
| C | Chimeric TCR VALPHA14JALPHA18 chain (mouse variable, human constant domain) | protein | 202 | 3% helix, 48% strand | — |
| D | Chimeric TCR VBETA8.2 chain (mouse variable, human constant domain) | protein | 239 | 6% helix, 49% strand | — |
Ligands and binding sites
- 49Y · (4Z)-9-[(1R,2R)-2-decylcyclopropyl]-N-[(2S,3S,4S)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]non-4-enamide · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.86 | 0.87 | 78 | 49Y |
| 2 | 779 | 0.65 | 0.74 | 67 | empty |
| 3 | 431 | 0.64 | 0.77 | 50 | empty |
| 4 | 178 | 0.46 | 0.75 | 31 | empty |
| 5 | 123 | 0.45 | 0.77 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2083 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1088 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 476 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 354 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4Y4K · Crystal structure of the mCD1d/EF77/iNKTCR ternary complex · the same entry in another collection · chain A against A, 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 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P01887
- Elsewhere: RCSB PDB 4Y4K · PDBe 4Y4K · UniProt P11609 · UniProt P01887
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