Research workbench
The crystal structure of human CD1D with and without alpha- galactosylceramide
Analyse The crystal structure of human CD1D with and without alpha- galactosylceramide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZT4
- Type
- protein
- Length
- 750 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1D; Beta-2-microglobulin
- UniProt
- P15813, P61769
- Ligands
- AGH
- Pockets
- 12 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1D | protein | 272 | 24% helix, 37% strand | P15813 |
| B, D | Beta-2-microglobulin | protein | 100 | 0% helix, 46% strand | P61769 |
| C | T-cell surface glycoprotein CD1D | protein | 278 | 26% helix, 36% strand | P15813 |
Ligands and binding sites
- AGH · N-{(1S,2R,3S)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}hexacosanamide · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.88 | 0.93 | 57 | AGH |
| 2 | 716 | 0.83 | 0.86 | 65 | empty |
| 3 | 447 | 0.82 | 0.89 | 58 | empty |
| 4 | 207 | 0.65 | 0.84 | 28 | empty |
| 5 | 334 | 0.63 | 0.79 | 41 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1406 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1324 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1049 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 302 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 131 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1ZT4 · The crystal structure of human CD1d with and without alpha-Galactosylceramide · the same entry in another collection · chain D against D, 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 0.97
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 1ZT4 · PDBe 1ZT4 · UniProt P15813 · UniProt P61769
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