Research workbench
Crystal Structure of Human CD1b in Complex with PA
Analyse Crystal Structure of Human CD1b in Complex with PA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WKG
- Type
- protein
- Length
- 377 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.06
- Source
- Homo sapiens
- Molecule
- T-cell surface glycoprotein CD1b; Beta-2-microglobulin
- UniProt
- P29016, P61769
- Ligands
- D21, CUY, NAG, FUC, MAN, BMA, NA, CL, IOD
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · resolution 2.06 · 2 distinct chains · 19% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1b | protein | 280 | 25% helix, 42% strand | P29016 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 51% strand | P61769 |
Ligands and binding sites
- D21 · (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate · ligand · chains A
- CUY · tetracosyl octadecanoate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B
- IOD · Iodide ion · ion · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- EDO · 1,2-ethanediol · additive · 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 | 734 | 0.87 | 0.90 | 69 | D21, CUY |
| 2 | 382 | 0.65 | 0.79 | 46 | empty |
| 3 | 147 | 0.45 | 0.76 | 28 | empty |
| 4 | 135 | 0.44 | 0.76 | 24 | EDO |
| 5 | 66 | 0.34 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1182 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5WKG · Crystal structure of human CD1B in complex with pa · 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
- 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 0.97
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 P29016
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 5WKG · PDBe 5WKG · UniProt P29016 · UniProt P61769
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