Research workbench
Crystal structure of Cardiolipin bound to mouse CD1D
Analyse Crystal structure of Cardiolipin bound to mouse CD1D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MA7
- Type
- protein
- Length
- 734 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.29
- Source
- Mus musculus
- Molecule
- T-cell surface glycoprotein CD1d1; Beta-2 microglobulin
- UniProt
- P11609, Q91XJ8
- Ligands
- CD4, PLM, NAG
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.29 · 3 distinct chains · 22% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | T-cell surface glycoprotein CD1d1 | protein | 265 | 27% helix, 41% strand | P11609 |
| D, B | Beta-2 microglobulin | protein | 98 | 0% helix, 50% strand | Q91XJ8 |
| A | T-cell surface glycoprotein CD1d1 | protein | 273 | 26% helix, 40% strand | P11609 |
Ligands and binding sites
- CD4 · (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate · ligand · 2 copies · chains C, A
- PLM · Palmitic acid · ligand · 2 copies · chains C, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains C, A
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 | 630 | 0.84 | 0.88 | 58 | CD4, PLM |
| 2 | 695 | 0.83 | 0.86 | 70 | CD4, PLM |
| 3 | 381 | 0.63 | 0.78 | 47 | empty |
| 4 | 323 | 0.62 | 0.79 | 34 | empty |
| 5 | 124 | 0.46 | 0.78 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1295 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1262 Ų buried · 19 hydrogen bonds · protein-protein
- C–A · 146 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3MA7 · Crystal structure of cardiolipin bound to mouse CD1D · 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 C 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 Q91XJ8
- Elsewhere: RCSB PDB 3MA7 · PDBe 3MA7 · UniProt P11609 · UniProt Q91XJ8
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