MolNFT v1 · #31137 · protein
Structural basis of sulfatide presentation by mouse CD1D
2AKR · T-cell surface glycoprotein CD1D1: “Structural basis of sulfatide presentation by mouse CD1D”. X-ray diffraction, 2 ligands (CIS, NAG), 9 pockets (best druggability 0.85). MolNFT v1 #31137 on GenesisL1: 3D structure, binding sites…
- PDB
- 2AKR
- Type
- protein
- Length
- 734 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1D1; Beta-2-microglobulin
- UniProt
- P11609
- Ligands
- CIS, NAG
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | T-cell surface glycoprotein CD1D1 | protein | 269 | 26% helix, 41% strand | P11609 |
| B, D | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | — |
Ligands and binding sites
- CIS · (15Z)-N-((1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-enyl)tetracos-15-enamide · ligand · 2 copies · chains A, C
- 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.85 | 0.91 | 54 | CIS |
| 2 | 592 | 0.83 | 0.88 | 57 | CIS |
| 3 | 775 | 0.71 | 0.77 | 80 | empty |
| 4 | 342 | 0.64 | 0.79 | 44 | empty |
| 5 | 162 | 0.47 | 0.76 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1257 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1255 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 327 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 2AKR · Structural basis of sulfatide presentation by 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 A against A, TM-score 0.99
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
- Elsewhere: RCSB PDB 2AKR · PDBe 2AKR · UniProt P11609
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