Research workbench
Crystal structure of mouse CD1D bound to the self ligand phosphatidylcholine
Analyse Crystal structure of mouse CD1D bound to the self ligand phosphatidylcholine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZHN
- Type
- protein
- Length
- 369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD1D1 antigen; Beta-2-microglobulin
- UniProt
- P01887
- Ligands
- PC6, NAG, MAN, FUC
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD1D1 antigen | protein | 270 | 26% helix, 42% strand | — |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
Ligands and binding sites
- PC6 · 7-[(dodecanoyloxy)methyl]-4-hydroxy-N,N,N-trimethyl-9-oxo-3,5,8-trioxa-4-phosphadotriacontan-1-aminium 4-oxide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.84 | 0.88 | 57 | PC6 |
| 2 | 350 | 0.64 | 0.79 | 46 | GOL |
| 3 | 135 | 0.46 | 0.77 | 19 | empty |
| 4 | 111 | 0.40 | 0.76 | 22 | empty |
| 5 | 60 | 0.31 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1315 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 1ZHN · Crystal Structure of mouse CD1d bound to the self ligand phosphatidylcholine · 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 0.98
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 P01887
- Elsewhere: RCSB PDB 1ZHN · PDBe 1ZHN · UniProt P01887
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