MolNFT v1 · #91241 · protein
Crystal structure of bovine CD1D with bound C12-di-sulfatide
4F7C · CD1D antigen, D polypeptide: “Crystal structure of bovine CD1D with bound C12-di-sulfatide”. X-ray diffraction, 3 ligands (0SG, NAG, BMA), 10 pockets (best druggability 0.86). MolNFT v1 #91241 on GenesisL1: 3D structure, binding…
- PDB
- 4F7C
- Type
- protein
- Length
- 726 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD1D antigen, D polypeptide; Beta-2-microglobulin
- UniProt
- A1L565, P01888
- Ligands
- 0SG, NAG, BMA
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD1D antigen, D polypeptide | protein | 269 | 26% helix, 40% strand | A1L565 |
| B, D | Beta-2-microglobulin | protein | 97 | 0% helix, 54% strand | P01888 |
| C | CD1D antigen, D polypeptide | protein | 263 | 26% helix, 40% strand | A1L565 |
Ligands and binding sites
- 0SG · N-{(2S,3R,4E)-1-[(3,6-di-O-sulfo-beta-D-galactopyranosyl)oxy]-3-hydroxyoctadec-4-en-2-yl}dodecanamide · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.86 | 0.90 | 58 | 0SG |
| 2 | 626 | 0.86 | 0.90 | 55 | 0SG |
| 3 | 326 | 0.61 | 0.78 | 42 | empty |
| 4 | 388 | 0.61 | 0.77 | 49 | empty |
| 5 | 208 | 0.46 | 0.74 | 36 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1492 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1469 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 150 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 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 A1L565
- Every structure of UniProt P01888
- Elsewhere: RCSB PDB 4F7C · PDBe 4F7C · UniProt A1L565 · UniProt P01888
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