Research workbench
Lectin pa-iil of P.AERUGINOSA complexed with disaccharide derivative
Analyse Lectin pa-iil of P.AERUGINOSA complexed with disaccharide derivative in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JDK
- 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
- T45, FUC, NAG, 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 | Fucose-binding lectin pa-iil | protein | 114 | 0% helix, 71% strand | Q9HYN5 |
Ligands and binding sites
- T45 · Methyl 2H-1,2,3-triazole-4-carboxylate · ligand · 3 copies
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains 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 | 91 | 0.33 | 0.74 | 19 | empty |
| 2 | 75 | 0.28 | 0.72 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1342 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1342 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 527 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 520 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 228 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2JDK · Lectin PA-IIL of P.aeruginosa complexed with disaccharide derivative · 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 2JDK · PDBe 2JDK · UniProt Q9HYN5
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