MolNFT v1 · #119792 · protein
Crystal structure of langerin carbohydrate recognition domain with GLCNS6S
5G6U: “Crystal structure of langerin carbohydrate recognition domain with GLCNS6S”. X-ray diffraction, 5 ligands (TRP, SGN, EU), 6 pockets (best druggability 0.77). MolNFT v1 #119792 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5G6U
- Type
- protein
- Length
- 514 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Langerin
- UniProt
- Q9UJ71
- Ligands
- TRP, SGN, EU, CA, CL
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Langerin | protein | 131 | 24% helix, 31% strand | Q9UJ71 |
| B, C | Langerin | protein | 128 | 24% helix, 31% strand | Q9UJ71 |
| D | Langerin | protein | 127 | 24% helix, 31% strand | Q9UJ71 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 3 copies · chains A, C, B, D
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- EU · Europium ion · metal · 6 copies · chains A, B, C
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 12 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 | 618 | 0.77 | 0.83 | 93 | empty |
| 2 | 513 | 0.76 | 0.84 | 71 | empty |
| 3 | 182 | 0.57 | 0.81 | 31 | TRP |
| 4 | 87 | 0.38 | 0.77 | 17 | TRP |
| 5 | 52 | 0.31 | 0.77 | 17 | TRP |
Interfaces
4 interfaces between chains.
- A–C · 701 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 679 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 671 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 637 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5G6U · Crystal structure of langerin carbohydrate recognition domain with GlcNS6S · the same entry in another collection · chain B against B, 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 5G6U · PDBe 5G6U · UniProt Q9UJ71
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