MolNFT v1 · #65085 · protein
Structure of mouse CD1D in complex with pbs-25
3GMP · T-cell surface glycoprotein CD1D1: “Structure of mouse CD1D in complex with pbs-25”. X-ray diffraction, 6 ligands (PBS, PLM, NAG), 3 pockets (best druggability 0.84). MolNFT v1 #65085 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3GMP
- Type
- protein
- Length
- 367 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1D1; Beta-2 microglobulin
- UniProt
- P11609, Q91XJ8
- Ligands
- PBS, PLM, NAG, MAN, BMA, FUC
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1D1 | protein | 268 | 27% helix, 42% strand | P11609 |
| B | Beta-2 microglobulin | protein | 99 | 0% helix, 49% strand | Q91XJ8 |
Ligands and binding sites
- PBS · (2S,3S,4R)-N-octanoyl-1-[(alpha-D-galactopyranosyl) oxy]-2-amino-octadecane-3,4-diol · ligand · chains A
- PLM · Palmitic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 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 | 58 | PBS, PLM |
| 2 | 518 | 0.66 | 0.77 | 55 | EDO |
| 3 | 190 | 0.46 | 0.74 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1201 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
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 3GMP · PDBe 3GMP · UniProt P11609 · UniProt Q91XJ8
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