MolNFT v1 · #145808 · protein
Structure of sphingomyelin in complex with mouse CD1D
6CYW · Antigen-presenting glycoprotein CD1D1: “Structure of sphingomyelin in complex with mouse CD1D”. X-ray diffraction, 2 ligands (FO4, NAG), 4 pockets (best druggability 0.84). MolNFT v1 #145808 on GenesisL1: 3D structure, binding sites…
- PDB
- 6CYW
- Type
- protein
- Length
- 369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin
- UniProt
- A0A0R4J090, P01887
- Ligands
- FO4, NAG
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 271 | 26% helix, 42% strand | A0A0R4J090 |
| B | Beta-2-microglobulin | protein | 98 | 0% helix, 52% strand | P01887 |
Ligands and binding sites
- FO4 · sphingomyelin · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.84 | 0.88 | 58 | FO4 |
| 2 | 500 | 0.67 | 0.78 | 54 | empty |
| 3 | 129 | 0.44 | 0.76 | 17 | empty |
| 4 | 81 | 0.35 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1298 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
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 6CYW · PDBe 6CYW · UniProt A0A0R4J090 · UniProt P01887
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