MolNFT v1 · #138921 · protein

Luciferase with inhibitor 3I

5WYS · Luciferin 4-monooxygenase: “Luciferase with inhibitor 3I”. X-ray diffraction, 1 ligand (7V6), 7 pockets (best druggability 0.70). MolNFT v1 #138921 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5WYS
Type: protein
Length: 539 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Luciferin 4-monooxygenase
EC: 1.13.12.7
UniProt: P08659
Ligands: 7V6
Pockets: 7 · best druggability 0.70

Structure

x-ray diffraction · 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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