Research workbench
Structure of the lecb lectin from pseudomonas aeruginosa strain PA14 in complex with 3-thiophenesulfonamide-2,5-dimethyl-N-methyl-beta-L- fucopyranoside
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
- 5MAZ
- 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
- A0A0H2ZE85
- Ligands
- IGF, FUL, CA
- 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 | A0A0H2ZE85 |
Ligands and binding sites
- IGF · N,2,5-trimethyl-3-thiophenesulfonamide · ligand · 4 copies · chains A, B, C, D
- FUL · beta-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains B, D
- GOL · Glycerol · 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 | 119 | 0.36 | 0.73 | 18 | empty |
| 2 | 106 | 0.35 | 0.73 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1314 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1294 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 470 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 467 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 231 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5MAZ · 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 A0A0H2ZE85
- Elsewhere: RCSB PDB 5MAZ · PDBe 5MAZ · UniProt A0A0H2ZE85
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