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PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 157)

Analyse PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5PLZ
Type: protein
Length: 331 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.71
Source: Homo sapiens
Molecule: Lysine-specific demethylase 4D
UniProt: Q6B0I6
Ligands: OGA, ZN, NI, MG, SO4
Pockets: 2 · best druggability 0.75

Structure

x-ray diffraction · resolution 1.71 · 1 distinct chain · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific demethylase 4D	protein	331	32% helix, 26% strand	Q6B0I6

Ligands and binding sites

OGA · N-oxalylglycine · ligand · chains A
ZN · Zinc ion · metal · chains A
NI · Nickel (II) ion · metal · chains A
MG · Magnesium ion · metal · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A
EDO · 1,2-ethanediol · additive · 8 copies · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	429	0.75	0.85	50	NI, OGA, EDO
2	83	0.38	0.77	24	EDO

Compared structures

5PLZ · Pandda analysis group deposition -- crystal structure of JMJD2D after initial refinement… · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt Q6B0I6
Elsewhere: RCSB PDB 5PLZ · PDBe 5PLZ · UniProt Q6B0I6

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