Research workbench
Structure of the PL6 family alginate lyase PEDSA0632 from pseudopedobacter saltans in complex with substrate
Analyse Structure of the PL6 family alginate lyase PEDSA0632 from pseudopedobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O84
- Type
- protein
- Length
- 817 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alginate lyase
- UniProt
- F0S7Y7
- Ligands
- LGU, MAW
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alginate lyase | protein | 410 | 4% helix, 42% strand | F0S7Y7 |
| B | Alginate lyase | protein | 407 | 4% helix, 41% strand | F0S7Y7 |
Ligands and binding sites
- LGU · alpha-L-gulopyranuronic acid · ligand · 5 copies · chains A, B
- MAW · 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.76 | 0.79 | 84 | LGU |
| 2 | 54 | 0.30 | 0.75 | 18 | empty |
| 3 | 58 | 0.29 | 0.74 | 17 | empty |
| 4 | 50 | 0.26 | 0.73 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 357 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7O84 · Structure of the PL6 family alginate lyase Pedsa0632 from Pseudopedobacter saltans in… · 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 F0S7Y7
- Elsewhere: RCSB PDB 7O84 · PDBe 7O84 · UniProt F0S7Y7
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