MolNFT v1 · #79377 · protein
Crystal structure of the mouse CD1D-glc-dag-S2 complex
3T1F · Antigen-presenting glycoprotein CD1D1: “Crystal structure of the mouse CD1D-glc-dag-S2 complex”. X-ray diffraction, 2 ligands (3TF, NAG), 4 pockets (best druggability 0.83). MolNFT v1 #79377 on GenesisL1: 3D structure, binding sites…
- PDB
- 3T1F
- Type
- protein
- Length
- 362 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin
- UniProt
- P11609, P01887
- Ligands
- 3TF, NAG
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 44% 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 |
Ligands and binding sites
- 3TF · (2S)-1-(alpha-D-glucopyranosyloxy)-3-(hexadecanoyloxy)propan-2-yl (11Z)-octadec-11-enoate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.83 | 0.87 | 60 | 3TF |
| 2 | 383 | 0.65 | 0.79 | 43 | GOL |
| 3 | 150 | 0.47 | 0.77 | 23 | empty |
| 4 | 137 | 0.47 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1306 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3T1F · Crystal structure of the mouse CD1d-Glc-DAG-s2 complex · 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 3T1F · PDBe 3T1F · UniProt P11609 · UniProt P01887
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