MolNFT v1 · #145711 · protein
Structure of alpha-GC[8,18] bound by CD1D and in complex with the VA14VB8.2 TCR
6CW6 · Antigen-presenting glycoprotein CD1D1: “Structure of alpha-GC[8,18] bound by CD1D and in complex with the VA14VB8.2 TCR”. X-ray diffraction, 4 ligands (PBS, PLM, NAG), 7 pockets (best druggability 0.86). MolNFT v1 #145711 on…
- PDB
- 6CW6
- Type
- protein
- Length
- 806 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; Chimeric T cell antigen…
- UniProt
- P11609, P01887, K7N5M3, K7N5M4
- Ligands
- PBS, PLM, NAG, FUC
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 268 | 27% helix, 40% strand | P11609 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 51% strand | P01887 |
| C | Chimeric T cell antigen receptor alpha chain | protein | 202 | 5% helix, 47% strand | K7N5M3 |
| D | Chimeric T cell antigen receptor beta chain VB8.2 | protein | 239 | 6% helix, 49% strand | K7N5M4 |
Ligands and binding sites
- PBS · (2S,3S,4R)-N-octanoyl-1-[(alpha-D-galactopyranosyl) oxy]-2-amino-octadecane-3,4-diol · ligand · chains A, C
- PLM · Palmitic acid · ligand · chains A
- 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.86 | 0.87 | 77 | PBS, PLM |
| 2 | 904 | 0.69 | 0.75 | 72 | empty |
| 3 | 452 | 0.66 | 0.78 | 52 | empty |
| 4 | 224 | 0.51 | 0.76 | 34 | empty |
| 5 | 115 | 0.45 | 0.78 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2107 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1181 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 484 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 392 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6CW6 · Structure of alpha-GC[8,18] bound by CD1d and in complex with the Va14Vb8.2 TCR · 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
- Every structure of UniProt K7N5M3
- Every structure of UniProt K7N5M4
- Elsewhere: RCSB PDB 6CW6 · PDBe 6CW6 · UniProt P11609 · UniProt P01887 · UniProt K7N5M3 · UniProt K7N5M4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.