Research workbench
Structure of human CD1D-sulfatide
Analyse Structure of human CD1D-sulfatide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MQ7
- Type
- protein
- Length
- 366 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D, CD1D1 protein; Beta-2-microglobulin
- UniProt
- P15813, Q7TMK5, P01887
- Ligands
- CIS, NAG
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D, CD1D1 protein | protein | 268 | 26% helix, 40% strand | P15813, Q7TMK5 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 52% strand | P01887 |
Ligands and binding sites
- CIS · (15Z)-N-((1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-enyl)tetracos-15-enamide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.86 | 0.91 | 55 | CIS |
| 2 | 379 | 0.67 | 0.80 | 50 | empty |
| 3 | 194 | 0.53 | 0.78 | 28 | empty |
| 4 | 157 | 0.48 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1281 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4MQ7 · Structure of human CD1d-sulfatide · the same entry in another collection · chain B against B, TM-score 1.00
- P15813 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D (P15813) · a predicted model of the same protein · chain A against A, TM-score 0.98
- 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 P15813
- Every structure of UniProt Q7TMK5
- Every structure of UniProt P01887
- Elsewhere: RCSB PDB 4MQ7 · PDBe 4MQ7 · UniProt P15813 · UniProt Q7TMK5 · UniProt P01887
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