MolNFT v1 · #113047 · protein
Crystal structure of the lecb lectin from pseudomonas aeruginosa in complex with methyl 6-(cinnamido)-6-deoxy-alpha-D-mannopyranoside at 1.6 ansgtrom
5A3O · Fucose-binding lectin pa-iil: “Crystal structure of the lecb lectin from pseudomonas aeruginosa in complex with methyl…”. X-ray diffraction, 4 ligands (DH6, MMA, CA), 2 pockets (best druggability 0.31). MolNFT v1 #113047 on…
- PDB
- 5A3O
- 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
- Q9HYN5
- Ligands
- DH6, MMA, CA, CL
- Pockets
- 2 · best druggability 0.31
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 62% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fucose-binding lectin pa-iil | protein | 114 | 0% helix, 62% strand | Q9HYN5 |
Ligands and binding sites
- DH6 · Cinnamide · ligand · 4 copies · chains A, B, C, D
- MMA · methyl alpha-D-mannopyranoside · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, D, B, C
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 | 87 | 0.31 | 0.73 | 18 | empty |
| 2 | 82 | 0.31 | 0.73 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1376 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1362 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 519 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 516 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 237 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5A3O · Crystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl… · 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 Q9HYN5
- Elsewhere: RCSB PDB 5A3O · PDBe 5A3O · UniProt Q9HYN5
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