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Crystal structure of the tudor domain of human JMJD2C

Analyse Crystal structure of the tudor domain of human JMJD2C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XDP
Type: protein
Length: 119 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific demethylase 4C
EC: 1.14.11.-
UniProt: Q9H3R0
Ligands: SO4
Pockets: 2 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific demethylase 4C (EC 1.14.11.-)	protein	119	8% helix, 41% strand	Q9H3R0

Ligands and binding sites

SO4 · Sulfate ion · ion · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	152	0.45	0.75	20	empty
2	60	0.32	0.76	12	empty

Compared structures

2XDP · Crystal structure of the tudor domain of human JMJD2C · the same entry in another collection · chain A against A, TM-score 1.00
Q9H3R0 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 4C (Q9H3R0) · a predicted model of the same protein · chain A against A, TM-score 0.66

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 Q9H3R0
Elsewhere: RCSB PDB 2XDP · PDBe 2XDP · UniProt Q9H3R0

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