Research workbench
Structure of the endogenous inkt cell ligand IGB3 bound to MCD1D
Analyse Structure of the endogenous inkt cell ligand IGB3 bound to MCD1D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q7Y
- Type
- protein
- Length
- 734 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1D1; Beta-2-microglobulin
- UniProt
- P11609, P01887
- Ligands
- IGC, PLM, NAG, MAN, BMA
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | T-cell surface glycoprotein CD1D1 | protein | 269 | 27% helix, 41% strand | P11609 |
| B, D | Beta-2-microglobulin | protein | 98 | 0% helix, 52% strand | P01887 |
Ligands and binding sites
- IGC · N-[(1S,2R,3E)-1-({[alpha-D-galactopyranosyl-(1->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl]oxy}methyl)-2-H ydroxyheptadec-3-en-1-yl]octanamide · ligand · 2 copies · chains A, C
- PLM · Palmitic acid · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.86 | 0.91 | 56 | IGC, PLM |
| 2 | 640 | 0.84 | 0.88 | 60 | IGC, PLM |
| 3 | 447 | 0.77 | 0.86 | 52 | empty |
| 4 | 428 | 0.67 | 0.80 | 49 | empty |
| 5 | 396 | 0.65 | 0.79 | 46 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1201 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1198 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 415 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 208 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 2Q7Y · Structure of the endogenous iNKT cell ligand iGb3 bound to mCD1d · the same entry in another collection · chain D against D, 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 0.98
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 2Q7Y · PDBe 2Q7Y · UniProt P11609 · UniProt P01887
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