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Structure-function analysis of a new PL17 oligoalginate lyase from the marine bacterium zobellia galactanivorans dsijt
Analyse Structure-function analysis of a new PL17 oligoalginate lyase from the marine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BJT
- Type
- protein
- Length
- 1,454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alginate lyase, family PL17
- EC
- 4.2.2.3
- UniProt
- G0LCA3
- Ligands
- MLT, MG, CA
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alginate lyase, family PL17 (EC 4.2.2.3) | protein | 727 | 34% helix, 26% strand | G0LCA3 |
Ligands and binding sites
- MLT · D-malate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.81 | 0.95 | 37 | MLT, GOL |
| 2 | 211 | 0.81 | 0.95 | 40 | MLT, GOL, MG |
| 3 | 1132 | 0.75 | 0.78 | 91 | empty |
| 4 | 397 | 0.72 | 0.83 | 61 | empty |
| 5 | 399 | 0.71 | 0.82 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 2294 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7BJT · Structure-function analysis of a new PL17 oligoalginate lyase from the marine bacterium… · 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 G0LCA3
- Elsewhere: RCSB PDB 7BJT · PDBe 7BJT · UniProt G0LCA3
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