Research workbench
Photorhabdus asymbiotica lectin (PHL) in complex with synthetic C-fucoside
Analyse Photorhabdus asymbiotica lectin (PHL) in complex with synthetic C-fucoside in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FHY
- Type
- protein
- Length
- 686 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.86
- Source
- Photorhabdus asymbiotica
- Molecule
- Lectin PHL
- UniProt
- C7BLE4
- Ligands
- DS8, CL
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.86 · 2 distinct chains · 0% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lectin PHL | protein | 342 | 0% helix, 45% strand | C7BLE4 |
| B | Lectin PHL | protein | 344 | 0% helix, 47% strand | C7BLE4 |
Ligands and binding sites
- DS8 · (2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[(2~{S},4~{R}, 6~{R})-2-(hydroxymethyl)-6-oxidanyl-oxan-4-yl]methyl]-6-methyl-oxane-3,4,5-triol · ligand · 12 copies · chains A, B
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.81 | 0.83 | 97 | empty |
| 2 | 570 | 0.80 | 0.86 | 38 | empty |
| 3 | 160 | 0.39 | 0.73 | 30 | CL |
| 4 | 59 | 0.37 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1109 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6FHY · Photorhabdus asymbiotica lectin (phl) in complex with synthetic C- fucoside · 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 C7BLE4
- Elsewhere: RCSB PDB 6FHY · PDBe 6FHY · UniProt C7BLE4
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