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Polygalacturonate Lyase by Fusing with a Self-assembling Amphipathic Peptide

Analyse Polygalacturonate Lyase by Fusing with a Self-assembling Amphipathic Peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5X2I
Type: protein
Length: 399 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.05
Source: Bacillus subtilis subsp. subtilis str. 168
Molecule: Pectate lyase
EC: 4.2.2.2
UniProt: P39116
Ligands: CA, CL
Pockets: 1 · best druggability 0.55

Structure

x-ray diffraction · resolution 2.05 · 1 distinct chain · 19% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pectate lyase (EC 4.2.2.2)	protein	399	19% helix, 32% strand	P39116

Ligands and binding sites

CA · Calcium ion · metal · chains A
CL · Chloride ion · ion · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	321	0.55	0.76	39	CL

Compared structures

5X2I · Polygalacturonate lyase by fusing with a self-assembling amphipathic peptide · the same entry in another collection · chain A against A, TM-score 1.00
P39116 · AlphaFold monomer V2.0 prediction for pectate lyase (P39116) · a predicted model of the same protein · 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 P39116
Elsewhere: RCSB PDB 5X2I · PDBe 5X2I · UniProt P39116

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