MolNFT v1 · #46289 · protein

Pectate lyase bound to hexasaccharide compound II

2O04: “Pectate lyase bound to hexasaccharide compound II”. X-ray diffraction, 2 ligands (ADA, CA), 2 pockets (best druggability 0.43). MolNFT v1 #46289 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2O04
Type: protein
Length: 399 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pectate lyase
EC: 4.2.2.2
UniProt: P39116
Ligands: ADA, CA
Pockets: 2 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pectate lyase (EC 4.2.2.2)	protein	399	18% helix, 31% strand	P39116

Ligands and binding sites

ADA · alpha-D-galactopyranuronic acid · sugar · 2 copies · chains A
CA · Calcium ion · metal · 3 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	165	0.43	0.74	27	ADA, CA
2	100	0.37	0.75	16	empty

Compared structures

2O04 · Pectate lyase bound to hexasaccharide compound II · 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 2O04 · PDBe 2O04 · UniProt P39116

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