MolNFT v2 · #139333 · protein
Crystal Structure of Human CD1b in Complex with PA
5WKG: “Crystal Structure of Human CD1b in Complex with PA”. X-ray diffraction at 2.06, 9 ligands (D21, CUY, NAG). MolNFT v2 #139333 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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
- UniProt
- P29016, P61769
- Ligands
- D21, CUY, NAG, FUC, MAN, BMA, NA, CL, IOD
Structure
x-ray diffraction · resolution 2.06 · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 280 | — | P29016 |
| B | — | protein | 97 | — | 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.
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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