Research workbench

Soybean lipoxygenase-1 - re-refinement

Analyse Soybean lipoxygenase-1 - re-refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PZW
Type: protein
Length: 820 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Seed lipoxygenase-1
EC: 1.13.11.12
UniProt: P08170
Ligands: FE2
Pockets: 18 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Seed lipoxygenase-1 (EC 1.13.11.12)	protein	820	43% helix, 15% strand	P08170

Ligands and binding sites

FE2 · Fe (II) ion · metal · chains A
EDO · 1,2-ethanediol · additive · 4 copies · chains A
ACT · Acetate ion · additive · chains A

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

Pockets

18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	804	0.83	0.86	74	EDO
2	72	0.75	0.98	21	empty
3	376	0.70	0.82	36	EDO
4	53	0.69	0.97	17	empty
5	232	0.52	0.76	32	empty

Compared structures

3PZW · Soybean lipoxygenase-1 - re-refinement · the same entry in another collection · chain A against A, TM-score 1.00
P08170 · AlphaFold monomer V2.0 prediction for seed linoleate 13S-lipoxygenase-1 (P08170) · 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 P08170
Elsewhere: RCSB PDB 3PZW · PDBe 3PZW · UniProt P08170

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