Research workbench
Structure of langerin crd I313 D288 complexed with me-glcnac
Analyse Structure of langerin crd I313 D288 complexed with me-glcnac in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N36
- 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
- 2F8, CA, MG
- 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
- 2F8 · methyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains 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 | 529 | 0.78 | 0.85 | 75 | empty |
| 2 | 398 | 0.77 | 0.87 | 59 | empty |
| 3 | 218 | 0.59 | 0.80 | 35 | empty |
| 4 | 182 | 0.57 | 0.81 | 26 | empty |
| 5 | 75 | 0.41 | 0.79 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–C · 705 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 694 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 674 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 588 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4N36 · Structure of langerin CRD I313 D288 complexed with Me-GlcNAc · 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 4N36 · PDBe 4N36 · UniProt Q9UJ71
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