Research workbench
Structure analysis of ALGQ2, a MACROMOLECULE(ALGINATE)-binding periplasmic protein of sphingomonas sp. A1., complexed with an alginate tetrasaccharide
Analyse Structure analysis of ALGQ2, a MACROMOLECULE(ALGINATE)-binding periplasmic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J1N
- Type
- protein
- Length
- 984 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALGQ2
- Ligands
- MAV, LGU, BEM, CA
- Pockets
- 5 · 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 | ALGQ2 | protein | 492 | 45% helix, 15% strand | — |
Ligands and binding sites
- MAV · alpha-D-mannopyranuronic acid · ligand · 4 copies · chains A, B
- 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.82 | 0.83 | 89 | MAV, LGU, BEM |
| 2 | 1186 | 0.79 | 0.81 | 103 | MAV, LGU, BEM |
| 3 | 516 | 0.71 | 0.80 | 64 | empty |
| 4 | 264 | 0.51 | 0.74 | 34 | empty |
| 5 | 69 | 0.35 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 385 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1J1N · Structure Analysis of AlgQ2, A Macromolecule(Alginate)-Binding Periplasmic Protein Of… · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 1J1N · PDBe 1J1N
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