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Crystal structure of wild type pd-L4 from phytolacca dioica leaves

Analyse Crystal structure of wild type pd-L4 from phytolacca dioica leaves in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Z4U
Type: protein
Length: 261 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosome-inactivating protein pd-L4
EC: 3.2.2.22
UniProt: P84854
Pockets: 1 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribosome-inactivating protein pd-L4 (EC 3.2.2.22)	protein	261	39% helix, 24% strand	P84854

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.48	0.81	18	EDO

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2Z4U · Crystal structure of wild type PD-L4 from Phytolacca dioica leaves · the same entry in another collection · chain A against A, TM-score 1.00
P84854 · AlphaFold monomer V2.0 prediction for ribosome-inactivating protein pd-L3/PD-L4 (P84854) · 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 P84854
Elsewhere: RCSB PDB 2Z4U · PDBe 2Z4U · UniProt P84854

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