Research workbench
Photorhabdus asymbiotica lectin (phl) in complex with propargyl- fucoside
Analyse Photorhabdus asymbiotica lectin (phl) in complex with propargyl- fucoside in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F5W
- Type
- protein
- Length
- 688 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin phl
- UniProt
- C7BLE4
- Ligands
- KG1, NA, CL
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lectin phl | protein | 344 | 0% helix, 47% strand | C7BLE4 |
Ligands and binding sites
- KG1 · propadienyl 6-deoxy-alpha-L-galactopyranoside · ligand · 11 copies · chains A, B
- NA · Sodium ion · metal · 9 copies · chains A, B
- CL · Chloride ion · ion · 11 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.81 | 0.83 | 104 | NA, CL, DMS |
| 2 | 616 | 0.80 | 0.86 | 41 | NA, CL |
| 3 | 128 | 0.36 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1103 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6F5W · Photorhabdus asymbiotica lectin (PHL) in complex with propargyl-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 6F5W · PDBe 6F5W · UniProt C7BLE4
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