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Crystal structure of human KDM4D in complex with 3- aminopyridine-4-carboxylic acid

Analyse Crystal structure of human KDM4D in complex with 3- aminopyridine-4-carboxylic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5FP9
Type: protein
Length: 327 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Human lysine-specific demethylase 4D jmjc domain-containing histone demethylation protein…
EC: 1.14.11.-
UniProt: Q6B0I6
Ligands: 4SV, ZN, CO, SO4
Pockets: 2 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Human lysine-specific demethylase 4D jmjc domain-containing histone demethylation protein 3D, jumonji domain-containing protein 2D, JMJD2D (EC 1.14.11.-)	protein	327	32% helix, 25% strand	Q6B0I6

Ligands and binding sites

4SV · 3-aminopyridine-4-carboxylic acid · ligand · chains A
ZN · Zinc ion · metal · chains A
CO · Cobalt (II) ion · metal · chains A
SO4 · Sulfate ion · ion · 7 copies · chains A
GOL · Glycerol · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	467	0.73	0.82	50	CO, 4SV, SO4
2	87	0.34	0.74	26	GOL

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

5FP9 · Crystal structure of human KDM4D in complex with 3-aminopyridine-4- carboxylic acid · the same entry in another collection · chain A against A, TM-score 1.00

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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 5FP9 · PDBe 5FP9 · UniProt Q6B0I6

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