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Crystal structure of the marine PL7 alginate lyase ALYA1 from zobellia galactanivorans
Analyse Crystal structure of the marine PL7 alginate lyase ALYA1 from zobellia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZPY
- Type
- protein
- Length
- 495 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alginate lyase, family PL7
- EC
- 4.2.2.3, 4.2.2.11
- UniProt
- G0LAE1
- Ligands
- NA
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alginate lyase, family PL7 (EC 4.2.2.3, 4.2.2.11) | protein | 248 | 6% helix, 48% strand | G0LAE1 |
| B | Alginate lyase, family PL7 (EC 4.2.2.3, 4.2.2.11) | protein | 247 | 5% helix, 48% strand | G0LAE1 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.69 | 0.78 | 72 | empty |
| 2 | 168 | 0.48 | 0.77 | 29 | empty |
| 3 | 52 | 0.34 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 700 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3ZPY · Crystal structure of the marine PL7 alginate lyase AlyA1 from Zobellia galactanivorans · 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 G0LAE1
- Elsewhere: RCSB PDB 3ZPY · PDBe 3ZPY · UniProt G0LAE1
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