MolNFT v2 · #130999 · protein

PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09552a

5PH8: “PanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09552a”. X-ray diffraction at 1.396, 6 ligands (OGA, PHT, 1XN). MolNFT v2 #130999 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5PH8
Type: protein
Length: 331 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.396
Source: Homo sapiens
UniProt: Q6B0I6
Ligands: OGA, PHT, 1XN, ZN, NI, SO4

Structure

x-ray diffraction · resolution 1.396 · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	331	—	Q6B0I6

Ligands and binding sites

OGA · N-oxalylglycine · ligand · chains A
PHT · Phthalic acid · ligand · chains A
1XN · 2H-isoindole-1,3-diamine · ligand · chains A
ZN · Zinc ion · metal · chains A
NI · Nickel (II) ion · metal · chains A
SO4 · Sulfate ion · ion · 4 copies · chains A
EDO · 1,2-ethanediol · additive · 6 copies · chains A

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

Compared structures

5PH8 · Pandda analysis group deposition -- crystal structure of JMJD2D in complex with N09552A · the same entry in another collection · chain A against A, TM-score 1.00
Q6B0I6 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 4D (Q6B0I6) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 Q6B0I6
Elsewhere: RCSB PDB 5PH8 · PDBe 5PH8 · UniProt Q6B0I6

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