Research workbench
Structure of alpha-GSA[16,6P] bound by CD1D and in complex with the VA14VB8.2 TCR
Analyse Structure of alpha-GSA[16,6P] bound by CD1D and in complex with the VA14VB8.2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CX9
- Type
- protein
- Length
- 804 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
- A0A0R4J090, P01887
- Ligands
- EM4, NAG, FUC, NA
- Pockets
- 8 · best druggability 0.85
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 | 266 | 27% helix, 41% strand | A0A0R4J090 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 48% strand | P01887 |
| C | Chimeric T cell antigen receptor alpha chain VA14,VA24, JA18 | protein | 201 | 5% helix, 48% strand | — |
| D | Chimeric T cell antigen receptor beta chain VB8.2, VB11 | protein | 239 | 6% helix, 49% strand | — |
Ligands and binding sites
- EM4 · N-[(2S,3S,4R)-3,4-dihydroxy-8-oxo-8-[(6-phenylhexyl) amino]-1-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}octan-2-yl]hexacosanamide · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- NA · Sodium ion · metal · 7 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.85 | 0.86 | 80 | EM4 |
| 2 | 890 | 0.69 | 0.75 | 67 | empty |
| 3 | 477 | 0.67 | 0.79 | 52 | empty |
| 4 | 232 | 0.52 | 0.76 | 33 | empty |
| 5 | 66 | 0.36 | 0.78 | 15 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2130 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1200 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 492 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 360 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6CX9 · Structure of alpha-GSA[16,6P] 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
- 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 A0A0R4J090
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 6CX9 · PDBe 6CX9 · UniProt A0A0R4J090 · UniProt P01887
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