Research workbench
Crystal structure of human CD1D-alpha-galactosylceramide in complex with semi-invariant nkt cell receptor
Analyse Crystal structure of human CD1D-alpha-galactosylceramide in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HUJ
- Type
- protein
- Length
- 1,633 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1D; Beta-2-microglobulin; NKT15 T cell receptor…
- UniProt
- P15813, P61769
- Ligands
- AGH, NAG, BMA, NDG, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1D | protein | 275 | 24% helix, 40% strand | P15813 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 53% strand | P61769 |
| C | T-cell surface glycoprotein CD1D | protein | 274 | 24% helix, 38% strand | P15813 |
| D | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| E | NKT15 T cell receptor alpha-chain | protein | 199 | 3% helix, 47% strand | — |
| F | NKT15 T cell receptor beta-chain | protein | 242 | 7% helix, 50% strand | — |
| G | NKT15 T cell receptor alpha-chain | protein | 202 | 1% helix, 47% strand | — |
| H | NKT15 T cell receptor beta-chain | protein | 245 | 6% helix, 49% strand | — |
Ligands and binding sites
- AGH · N-{(1S,2R,3S)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}hexacosanamide · ligand · 2 copies · chains A, G, C, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar
- MG · Magnesium ion · metal · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 815 | 0.87 | 0.89 | 82 | AGH |
| 2 | 899 | 0.86 | 0.88 | 91 | AGH |
| 3 | 816 | 0.82 | 0.85 | 88 | empty |
| 4 | 798 | 0.71 | 0.77 | 73 | empty |
| 5 | 860 | 0.70 | 0.76 | 79 | empty |
Interfaces
13 interfaces between chains.
- G–H · 2240 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 2121 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1330 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1222 Ų buried · 21 hydrogen bonds · protein-protein
- A–G · 470 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3HUJ · Crystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant… · the same entry in another collection · chain H against H, TM-score 1.00
- 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 0.98
- 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 3HUJ · PDBe 3HUJ · UniProt P15813 · UniProt P61769
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