MolNFT v1 · #25882 · protein
Structure of pseudomonas aeruginosa lectin II (pa-IIL)COMPLEXED with lewisa trisaccharide
1W8H: “Structure of pseudomonas aeruginosa lectin II (pa-IIL)COMPLEXED with lewisa trisaccharide”. X-ray diffraction, 6 ligands (GAL, FUC, NAG), 2 pockets (best druggability 0.33). MolNFT v1 #25882 on GenesisL1: 3D structure, binding sites…
- PDB
- 1W8H
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pseudomonas aeruginosa lectin II
- UniProt
- Q9HYN5
- Ligands
- GAL, FUC, NAG, NDG, CA, SO4
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 71% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pseudomonas aeruginosa lectin II | protein | 114 | 0% helix, 71% strand | Q9HYN5 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, D, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, D
- CA · Calcium ion · metal · 8 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains C, A
- GOL · Glycerol · additive · 3 copies · chains C, B, D
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 | 115 | 0.33 | 0.72 | 19 | empty |
| 2 | 98 | 0.33 | 0.73 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1345 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1340 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 528 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 523 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 228 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1W8H · structure of pseudomonas aeruginosa lectin II (PA-IIL)complexed with lewisA trisaccharide · 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 1W8H · PDBe 1W8H · UniProt Q9HYN5
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