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luciferase with inhibitor 3i

Analyse luciferase with inhibitor 3i in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WYS
Type: protein
Length: 539 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.999
Source: Photinus pyralis
Molecule: Luciferin 4-monooxygenase
EC: 1.13.12.7
UniProt: P08659
Ligands: 7V6
Pockets: 7 · best druggability 0.70

Structure

x-ray diffraction · resolution 2.999 · 1 distinct chain · 30% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Luciferin 4-monooxygenase (EC 1.13.12.7)	protein	539	30% helix, 24% strand	P08659

Ligands and binding sites

7V6 · 5-[(3R)-3-(4-boranylphenyl)-3-oxidanyl-propyl]-2-oxidanyl-benzoic acid · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	395	0.70	0.82	56	7V6
2	315	0.59	0.77	47	empty
3	69	0.45	0.82	14	empty
4	64	0.42	0.82	13	empty
5	51	0.38	0.81	15	empty

Compared structures

5WYS · Luciferase with inhibitor 3I · the same entry in another collection · chain A against A, TM-score 1.00
P08659 · AlphaFold monomer V2.0 prediction for luciferin 4-monooxygenase (P08659) · a predicted model of the same protein · chain A against A, TM-score 0.83

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 P08659
Elsewhere: RCSB PDB 5WYS · PDBe 5WYS · UniProt P08659

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