MolNFT v1 · #74733 · protein
Structure of the carbohydrate-recognition domain of human langerin with blood group B trisaccharide (gal ALPHA1-3(FUC ALPHA1-2)GAL)
3P5G · C-type lectin domain family 4 member K: “Structure of the carbohydrate-recognition domain of human langerin with blood group B trisaccharide (gal…”. X-ray diffraction, 4 ligands (FUC, GLA, GAL), 6 pockets (best druggability 0.79).…
- PDB
- 3P5G
- Type
- protein
- Length
- 514 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-type lectin domain family 4 member K
- UniProt
- Q9UJ71
- Ligands
- FUC, GLA, GAL, CA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | C-type lectin domain family 4 member K | protein | 128 | 23% helix, 31% strand | Q9UJ71 |
| C, D | C-type lectin domain family 4 member K | protein | 129 | 24% helix, 32% strand | Q9UJ71 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- GLA · alpha-D-galactopyranose · sugar · 3 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · chains A
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.79 | 0.81 | 105 | empty |
| 2 | 699 | 0.77 | 0.82 | 80 | empty |
| 3 | 235 | 0.57 | 0.79 | 28 | empty |
| 4 | 75 | 0.35 | 0.76 | 15 | empty |
| 5 | 55 | 0.31 | 0.77 | 22 | empty |
Interfaces
4 interfaces between chains.
- B–D · 714 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 696 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 653 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 625 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3P5G · Structure of the carbohydrate-recognition domain of human Langerin with Blood group B… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9UJ71 · AlphaFold monomer V2.0 prediction for C-type lectin domain family 4 member K (Q9UJ71) · a predicted model of the same protein · chain D 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 Q9UJ71
- Elsewhere: RCSB PDB 3P5G · PDBe 3P5G · UniProt Q9UJ71
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