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Structure of the human Langerin carbohydrate recognition domain in complex with maltose
Analyse Structure of the human Langerin carbohydrate recognition domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P7H
- Type
- protein
- Length
- 524 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Homo sapiens
- Molecule
- C-type lectin domain family 4 member K
- UniProt
- Q9UJ71
- Ligands
- GLC, CA
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.3 · 3 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-type lectin domain family 4 member K | protein | 135 | 23% helix, 30% strand | Q9UJ71 |
| B, D | C-type lectin domain family 4 member K | protein | 130 | 24% helix, 32% strand | Q9UJ71 |
| C | C-type lectin domain family 4 member K | protein | 129 | 24% helix, 32% strand | Q9UJ71 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 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 | 461 | 0.77 | 0.85 | 62 | empty |
| 2 | 435 | 0.76 | 0.85 | 59 | empty |
| 3 | 287 | 0.63 | 0.80 | 50 | empty |
| 4 | 185 | 0.57 | 0.81 | 28 | empty |
| 5 | 61 | 0.34 | 0.77 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 957 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 807 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 692 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 688 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 195 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 modified (disulfide, engineered).
Compared structures
- 3P7H · Structure of the human langerin carbohydrate recognition domain in complex with maltose · 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 0.97
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 Q9UJ71
- Elsewhere: RCSB PDB 3P7H · PDBe 3P7H · UniProt Q9UJ71
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