Research workbench
Structure of the carbohydrate-recognition domain of human langerin with MAN5 (man ALPHA1-3(MAN ALPHA1-6)MAN ALPHA1-6)(MAN- ALPHA1-3)MAN
Analyse Structure of the carbohydrate-recognition domain of human langerin with MAN5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P5D
- 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
- MAN, CA
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 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 | 24% helix, 31% strand | Q9UJ71 |
| C | C-type lectin domain family 4 member K | protein | 130 | 24% helix, 32% strand | Q9UJ71 |
| D | C-type lectin domain family 4 member K | protein | 128 | 24% helix, 32% strand | Q9UJ71 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A, B, C, D
- 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.78 | 0.85 | 68 | empty |
| 2 | 477 | 0.77 | 0.85 | 73 | empty |
| 3 | 177 | 0.57 | 0.81 | 27 | empty |
| 4 | 173 | 0.56 | 0.81 | 28 | empty |
| 5 | 70 | 0.33 | 0.75 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–C · 711 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 705 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 672 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 605 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3P5D · Structure of the carbohydrate-recognition domain of human Langerin with man5 (Man… · 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 3P5D · PDBe 3P5D · UniProt Q9UJ71
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