Research workbench
Crystal structure of the MCD1D/GCK127/INKTCR ternary complex
Analyse Crystal structure of the MCD1D/GCK127/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
- 4Y4F
- Type
- protein
- Length
- 1,608 residues
- Chains
- 8
- 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
- 49M, NAG
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Antigen-presenting glycoprotein CD1D1 | protein | 267 | 26% helix, 40% strand | P11609 |
| B, F | Beta-2-microglobulin | protein | 96 | 0% helix, 53% strand | P01887 |
| C, G | Chimeric TCR VALPHA14/JALPHA18 chain (mouse variable domain/ human constant domain) | protein | 202 | 4% helix, 48% strand | — |
| D, H | Chimeric TCR VBETA8.2 chain (mouse variable domain, human constant domain) | protein | 239 | 6% helix, 49% strand | — |
Ligands and binding sites
- 49M · (1R)-1,5-anhydro-1-[(1E,3S,4S,5R)-4,5-dihydroxy-3-(nonacosanoylamino)nonadec-1-en-1-yl]-D-galactitol · ligand · 2 copies · chains A, C, E, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.86 | 0.88 | 75 | 49M |
| 2 | 871 | 0.86 | 0.87 | 76 | 49M |
| 3 | 1072 | 0.78 | 0.80 | 110 | empty |
| 4 | 932 | 0.69 | 0.74 | 80 | empty |
| 5 | 864 | 0.69 | 0.75 | 65 | empty |
Interfaces
11 interfaces between chains.
- C–D · 2137 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 2129 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1168 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1146 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 473 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4Y4F · Crystal structure of the mCD1d/GCK127/iNKTCR ternary 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
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 4Y4F · PDBe 4Y4F · UniProt P11609 · UniProt P01887
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