Research workbench
Structure of the lecb lectin from pseudomonas aeruginosa strain PA14 in complex with mannose-ALPHA1,3MANNOSIDE
Analyse Structure of the lecb lectin from pseudomonas aeruginosa strain PA14 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A6Y
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin pa-iil
- UniProt
- U8MRX2
- Ligands
- MAN, CA, SO4
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 71% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fucose-binding lectin pa-iil | protein | 114 | 0% helix, 71% strand | U8MRX2 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains B, A, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains C
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.36 | 0.73 | 18 | empty |
| 2 | 87 | 0.32 | 0.74 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1326 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1319 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 476 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 474 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 221 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5A6Y · Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with… · 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 U8MRX2
- Elsewhere: RCSB PDB 5A6Y · PDBe 5A6Y · UniProt U8MRX2
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