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Crystal structure of sphingomonas sp. A1 alginate-binding protein ALGQ1 in complex with mannuronate-guluronate disaccharide
Analyse Crystal structure of sphingomonas sp. A1 alginate-binding protein ALGQ1 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VLW
- Type
- protein
- Length
- 978 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALGQ1
- UniProt
- Q9KWT6
- Ligands
- LGU, BEM, CA
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ALGQ1 | protein | 489 | 45% helix, 15% strand | Q9KWT6 |
Ligands and binding sites
- LGU · alpha-L-gulopyranuronic acid · ligand · 2 copies · chains A, B
- BEM · beta-D-mannopyranuronic acid · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 18 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.82 | 0.83 | 88 | LGU, BEM, GOL |
| 2 | 1159 | 0.81 | 0.83 | 89 | LGU, BEM, GOL |
| 3 | 269 | 0.59 | 0.79 | 32 | empty |
| 4 | 371 | 0.57 | 0.75 | 37 | empty |
| 5 | 61 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 574 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3VLW · Crystal structure of Sphingomonas sp. A1 alginate-binding protein AlgQ1 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 Q9KWT6
- Elsewhere: RCSB PDB 3VLW · PDBe 3VLW · UniProt Q9KWT6
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