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Crystal structure of human JMJD2D in complex with 2,4-pdca

Analyse Crystal structure of human JMJD2D in complex with 2,4-pdca in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4D6Q
Type: protein
Length: 330 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific demethylase 4D
UniProt: Q6B0I6
Ligands: PD2, ZN, NI, SO4
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific demethylase 4D	protein	330	31% helix, 26% strand	Q6B0I6

Ligands and binding sites

PD2 · Pyridine-2,4-dicarboxylic acid · ligand · chains A
ZN · Zinc ion · metal · chains A
NI · Nickel (II) ion · metal · chains A
SO4 · Sulfate ion · ion · chains A
EDO · 1,2-ethanediol · additive · 5 copies · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	389	0.75	0.85	44	NI, PD2, EDO
2	58	0.46	0.84	19	empty
3	66	0.33	0.76	23	EDO

Compared structures

4D6Q · crystal structure of human JMJD2D in complex with 2,4-PDCA · 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 Q6B0I6
Elsewhere: RCSB PDB 4D6Q · PDBe 4D6Q · UniProt Q6B0I6

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