MolNFT v1 · #167007 · protein
Human CD1D presenting alpha-galactosylceramide in complex with vhh nanobody 1D22
6V7Z · Antigen-presenting glycoprotein CD1D: “Human CD1D presenting alpha-galactosylceramide in complex with vhh nanobody 1D22”. X-ray diffraction, 7 ligands (AGH, NAG, BMA), 11 pockets (best druggability 0.85). MolNFT v1 #167007 on…
- PDB
- 6V7Z
- Type
- protein
- Length
- 967 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antigen-presenting glycoprotein CD1D; Beta-2-microglobulin; Nanobody vhh ID22
- UniProt
- P15813, P61769
- Ligands
- AGH, NAG, BMA, BGC, NA, CL, SO4
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 17% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antigen-presenting glycoprotein CD1D | protein | 275 | 27% helix, 40% strand | P15813 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | Antigen-presenting glycoprotein CD1D | protein | 263 | 25% helix, 40% strand | P15813 |
| D | Beta-2-microglobulin | protein | 96 | 0% helix, 51% strand | P61769 |
| E, F | Nanobody vhh ID22 | protein | 117 | 5% helix, 56% strand | — |
Ligands and binding sites
- AGH · N-{(1S,2R,3S)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}hexacosanamide · ligand · 2 copies · chains A, C, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
- BGC · beta-D-glucopyranose · sugar · chains A, B
- NA · Sodium ion · metal · chains D
- CL · Chloride ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.85 | 0.90 | 54 | AGH |
| 2 | 1158 | 0.84 | 0.85 | 97 | AGH |
| 3 | 327 | 0.62 | 0.78 | 43 | BGC |
| 4 | 236 | 0.60 | 0.80 | 34 | empty |
| 5 | 234 | 0.54 | 0.77 | 33 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1299 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1225 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 860 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 819 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 513 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6V7Z · Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D22 · the same entry in another collection · chain F against F, TM-score 1.00
- P15813 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D (P15813) · a predicted model of the same protein · chain C against A, TM-score 0.99
- 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
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 6V7Z · PDBe 6V7Z · UniProt P15813 · UniProt P61769
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