Research workbench
Crystal structure of mouse CD1D in complex with the P99P lipopeptide
Analyse Crystal structure of mouse CD1D in complex with the P99P lipopeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EFI
- Type
- protein
- Length
- 378 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; P99P
- UniProt
- P11609, P01887
- Ligands
- PLM, OCA, NAG, MAN, BMA, FUC, NA
- Pockets
- 6 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D1 | protein | 263 | 27% helix, 42% strand | P11609 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C | P99P | protein | 16 | 56% helix, 0% strand | — |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A, C
- OCA · Octanoic acid (caprylic acid) · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
- NA · Sodium ion · metal · chains A
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.88 | 0.94 | 54 | CIT, PLM, OCA |
| 2 | 324 | 0.63 | 0.79 | 47 | empty |
| 3 | 190 | 0.47 | 0.75 | 28 | empty |
| 4 | 73 | 0.33 | 0.75 | 18 | empty |
| 5 | 63 | 0.33 | 0.76 | 10 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1267 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 874 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan, 1 lipid (disulfide, N-glycosylation, palmitoylation).
Compared structures
- 5EFI · Crystal structure of mouse CD1d in complex with the p99p lipopeptide · the same entry in another collection · chain A against A, 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 5EFI · PDBe 5EFI · UniProt P11609 · UniProt P01887
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