Research workbench
Photorhabdus laumondii lectin PLL2 in complex with O-methylated pgl-1- derived disaccharide
Analyse Photorhabdus laumondii lectin PLL2 in complex with O-methylated pgl-1- derived… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RGG
- Type
- protein
- Length
- 679 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin PLL2 from photorhabdus laumondii
- UniProt
- Q7N8I8
- Ligands
- K3Q, 7CV, NA
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lectin PLL2 from photorhabdus laumondii | protein | 340 | 0% helix, 46% strand | Q7N8I8 |
| B | Lectin PLL2 from photorhabdus laumondii | protein | 339 | 0% helix, 48% strand | Q7N8I8 |
Ligands and binding sites
- K3Q · 3,6-O-dimethyl-D-glucose · ligand · 6 copies · chains A, B
- 7CV · 6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.81 | 0.88 | 40 | empty |
| 2 | 515 | 0.80 | 0.86 | 43 | empty |
| 3 | 516 | 0.67 | 0.78 | 76 | empty |
Interfaces
1 interface between chains.
- A–B · 1089 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6RGG · Photorhabdus laumondii lectin PLL2 in complex with O-methylated PGL-1-derived disaccharide · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7N8I8
- Elsewhere: RCSB PDB 6RGG · PDBe 6RGG · UniProt Q7N8I8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.