Research workbench
Structure of a highly potent short-chain galactosyl ceramide agonist bound to CD1D
Analyse Structure of a highly potent short-chain galactosyl ceramide agonist bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z5L
- Type
- protein
- Length
- 727 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1D antigen; Beta-2-microglobulin
- Ligands
- PBS, R16, NAG
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1D antigen | protein | 265 | 26% helix, 42% strand | — |
| B, D | Beta-2-microglobulin | protein | 98 | 0% helix, 52% strand | — |
| C | T-cell surface glycoprotein CD1D antigen | protein | 266 | 26% helix, 43% strand | — |
Ligands and binding sites
- PBS · (2S,3S,4R)-N-octanoyl-1-[(alpha-D-galactopyranosyl) oxy]-2-amino-octadecane-3,4-diol · ligand · 2 copies · chains A, C
- R16 · Hexadecane · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, C
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 | 597 | 0.86 | 0.90 | 57 | PBS, R16 |
| 2 | 580 | 0.85 | 0.89 | 56 | PBS, R16 |
| 3 | 909 | 0.74 | 0.78 | 96 | empty |
| 4 | 424 | 0.65 | 0.78 | 46 | empty |
| 5 | 141 | 0.44 | 0.76 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1299 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1233 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 297 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 72 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 1Z5L · Structure of a highly potent short-chain galactosyl ceramide agonist bound to CD1D · the same entry in another collection · chain C against C, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1Z5L · PDBe 1Z5L
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