Research workbench
Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with lewis a
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
- 5A6Z
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- PSEUDOMONAS AERUGINOSA
- Molecule
- Lecb
- UniProt
- U8MRX2
- Ligands
- GAL, NAG, FUC, GLA, CA, SO4
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · resolution 1.5 · 1 distinct chain · 0% helix, 71% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lecb | protein | 114 | 0% helix, 71% strand | U8MRX2 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 5 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- GLA · alpha-D-galactopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains 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 | 111 | 0.37 | 0.74 | 20 | empty |
| 2 | 80 | 0.31 | 0.74 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1335 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1329 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 474 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 469 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 220 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5A6Z · 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 5A6Z · PDBe 5A6Z · UniProt U8MRX2
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