MolNFT v1 · #183943 · protein
Structure of the PL6 family alginate lyase PEDSA0632 from pseudopedobacter saltans in complex with substrate
7O84: “Structure of the PL6 family alginate lyase PEDSA0632 from pseudopedobacter saltans in complex with substrate”. X-ray diffraction, 2 ligands (LGU, MAW), 4 pockets (best druggability 0.76). MolNFT v1 #183943 on GenesisL1: 3D…
- 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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