MolNFT v1 · #134497 · protein

Lipoxygenase-1 (soybean) at 293K

5T5V · Seed linoleate 13S-lipoxygenase-1: “Lipoxygenase-1 (soybean) at 293K”. X-ray diffraction, 1 ligand (FE), 20 pockets (best druggability 0.83). MolNFT v1 #134497 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5T5V
Type: protein
Length: 1,640 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Seed linoleate 13S-lipoxygenase-1
EC: 1.13.11.12
UniProt: P08170
Ligands: FE
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Seed linoleate 13S-lipoxygenase-1 (EC 1.13.11.12)	protein	820	42% helix, 15% strand	P08170
B	Seed linoleate 13S-lipoxygenase-1 (EC 1.13.11.12)	protein	820	42% helix, 15% strand	P08170

Ligands and binding sites

FE · Fe (III) ion · metal · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	659	0.83	0.88	56	empty
2	858	0.83	0.85	73	empty
3	1015	0.81	0.82	102	empty
4	55	0.73	0.99	17	empty
5	370	0.70	0.82	47	empty

Interfaces

1 interface between chains.

A–B · 534 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5T5V · Lipoxygenase-1 (soybean) at 293K · 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 5T5V · PDBe 5T5V · UniProt P08170

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