MolNFT v1 · #129480 · protein
Galacturonidase
5OLP · Pectate lyase: “Galacturonidase”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.70). MolNFT v1 #129480 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5OLP
- Type
- protein
- Length
- 864 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pectate lyase
- UniProt
- Q8A066
- Ligands
- CA
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pectate lyase | protein | 432 | 12% helix, 51% strand | Q8A066 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.70 | 0.81 | 42 | CA |
| 2 | 426 | 0.67 | 0.79 | 41 | CA |
| 3 | 547 | 0.66 | 0.77 | 57 | empty |
| 4 | 325 | 0.57 | 0.77 | 32 | empty |
| 5 | 101 | 0.40 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 313 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 5OLP · Galacturonidase · 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 Q8A066
- Elsewhere: RCSB PDB 5OLP · PDBe 5OLP · UniProt Q8A066
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