Research workbench
Crystal structure of human CD1B in complex with synthetic antigenic diacylsulfoglycolipid SGL12 and endogenous spacer
Analyse Crystal structure of human CD1B in complex with synthetic antigenic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T8X
- Type
- protein
- Length
- 750 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1B; Beta-2-microglobulin
- UniProt
- P29016, P61769
- Ligands
- T8X, ULI, NAG, FUC, BMA, MAN, SO4
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1B | protein | 275 | 25% helix, 43% strand | P29016 |
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| C | T-cell surface glycoprotein CD1B | protein | 277 | 27% helix, 42% strand | P29016 |
Ligands and binding sites
- T8X · 2-O-sulfo-alpha-D-glucopyranosyl 2-O-hexadecanoyl-3-O-[(2E,4S,6S,8S)-2,4,6,8-tetramethyltetracos-2-enoyl]-alpha-D-glucopyranoside · ligand · 2 copies · chains A, C
- ULI · tetracontane · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A, D, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.87 | 0.90 | 67 | T8X, ULI |
| 2 | 789 | 0.86 | 0.88 | 64 | T8X, ULI |
| 3 | 664 | 0.69 | 0.77 | 75 | empty |
| 4 | 320 | 0.64 | 0.80 | 38 | empty |
| 5 | 301 | 0.53 | 0.75 | 53 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1390 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1330 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 104 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 90 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3T8X · Crystal structure of human CD1b in complex with synthetic antigenic diacylsulfoglycolipid… · the same entry in another collection · chain D against D, TM-score 1.00
- P29016 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1B (P29016) · a predicted model of the same protein · chain A 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 0.99
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 P29016
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 3T8X · PDBe 3T8X · UniProt P29016 · UniProt P61769
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