Research workbench
Structure of alginate-binding protein ALGQ2 in complex with an alginate trisaccharide
Analyse Structure of alginate-binding protein ALGQ2 in complex with an alginate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H71
- Type
- protein
- Length
- 981 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALGQ2
- UniProt
- Q9KWT5
- Ligands
- MAW, BEM, CA, CL
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ALGQ2 | protein | 489 | 45% helix, 15% strand | Q9KWT5 |
| B | ALGQ2 | protein | 492 | 45% helix, 15% strand | Q9KWT5 |
Ligands and binding sites
- MAW · 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid · ligand · 2 copies · chains A, B
- BEM · beta-D-mannopyranuronic acid · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.84 | 0.85 | 89 | BEM, MAW |
| 2 | 1157 | 0.82 | 0.83 | 97 | BEM, MAW |
| 3 | 927 | 0.71 | 0.76 | 73 | empty |
| 4 | 59 | 0.36 | 0.79 | 19 | empty |
| 5 | 64 | 0.32 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 289 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5H71 · Structure of alginate-binding protein AlgQ2 in complex with an alginate 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 Q9KWT5
- Elsewhere: RCSB PDB 5H71 · PDBe 5H71 · UniProt Q9KWT5
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