MolNFT v1 · #174140 · protein
Structure-function analysis of a new PL17 oligoalginate lyase from the marine bacterium zobellia galactanivorans dsijt
7BM6 · Alginate lyase, family PL17: “Structure-function analysis of a new PL17 oligoalginate lyase from the marine bacterium zobellia…”. X-ray diffraction, 4 ligands (MAV, MAW, MG), 12 pockets (best druggability 0.82). MolNFT v1 #174140 on…
- PDB
- 7BM6
- 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
- MAV, MAW, MG, CA
- Pockets
- 12 · best druggability 0.82
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
- MAV · alpha-D-mannopyranuronic acid · ligand · 2 copies · chains A, B
- MAW · 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.82 | 0.94 | 45 | MAV, MAW |
| 2 | 232 | 0.81 | 0.94 | 38 | MAV, MAW |
| 3 | 1127 | 0.75 | 0.78 | 93 | MG |
| 4 | 264 | 0.72 | 0.86 | 38 | empty |
| 5 | 317 | 0.72 | 0.85 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 2342 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 7BM6 · 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 7BM6 · PDBe 7BM6 · UniProt G0LCA3
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