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Luciferin-regenerating enzyme solved by sad using synchrotron radiation at room temperature

Analyse Luciferin-regenerating enzyme solved by sad using synchrotron radiation at room… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5D9D
Type: protein
Length: 306 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Luciferin regenerating enzyme
UniProt: Q95YI4
Ligands: HG, MG
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Luciferin regenerating enzyme	protein	306	5% helix, 50% strand	Q95YI4

Ligands and binding sites

HG · Mercury (II) ion · metal · 3 copies · chains A
MG · Magnesium ion · metal · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A

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

Pockets

3 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	182	0.75	0.91	31	empty
2	254	0.67	0.83	31	MPD
3	55	0.31	0.76	19	empty

Compared structures

5D9D · Luciferin-regenerating enzyme solved by SAD using synchrotron radiation at room… · the same entry in another collection · 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 Q95YI4
Elsewhere: RCSB PDB 5D9D · PDBe 5D9D · UniProt Q95YI4

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