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Luciferin-regenerating enzyme solved by siras using xfel (refined against hg derivative data)

Analyse Luciferin-regenerating enzyme solved by siras using xfel (refined against hg… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5D9C
Type: protein
Length: 307 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: 2 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Luciferin regenerating enzyme	protein	307	5% helix, 51% strand	Q95YI4

Ligands and binding sites

HG · Mercury (II) ion · metal · 2 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

2 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	164	0.74	0.91	30	empty
2	269	0.65	0.82	31	MPD

Compared structures

5D9C · Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against Hg derivative… · 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 5D9C · PDBe 5D9C · UniProt Q95YI4

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