Research workbench
Human CD1D presenting alpha-galactosylceramide in complex with vhh nanobody 1D5
Analyse Human CD1D presenting alpha-galactosylceramide in complex with vhh nanobody 1D5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V7Y
- Type
- protein
- Length
- 496 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D; Beta-2-microglobulin; Nanobody vhh ID5
- UniProt
- P15813, P61769
- Ligands
- AGH, NAG, BMA, SO4, CL
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D | protein | 270 | 27% helix, 39% strand | P15813 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| F | Nanobody vhh ID5 | protein | 126 | 7% helix, 45% strand | — |
Ligands and binding sites
- AGH · N-{(1S,2R,3S)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}hexacosanamide · ligand · chains A, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.85 | 0.88 | 57 | AGH |
| 2 | 401 | 0.63 | 0.77 | 53 | empty |
| 3 | 145 | 0.44 | 0.76 | 21 | empty |
| 4 | 79 | 0.34 | 0.75 | 23 | empty |
| 5 | 67 | 0.31 | 0.75 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1239 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 842 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6V7Y · Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D5 · the same entry in another collection · chain A against A, TM-score 1.00
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P15813 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D (P15813) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P15813
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 6V7Y · PDBe 6V7Y · UniProt P15813 · UniProt P61769
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