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Crystal structure of hybrid tudor domain of human lysine demethylase KDM4B

Analyse Crystal structure of hybrid tudor domain of human lysine demethylase KDM4B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4UC4
Type: protein
Length: 218 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific demethylase 4B
EC: 1.14.11.-
UniProt: O94953
Pockets: 2 · best druggability 0.36

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lysine-specific demethylase 4B (EC 1.14.11.-)	protein	109	9% helix, 54% strand	O94953

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	119	0.36	0.73	22	empty
2	50	0.24	0.72	16	empty

Interfaces

1 interface between chains.

A–B · 521 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4UC4 · Crystal structure of hybrid tudor domain of human lysine demethylase KDM4B · the same entry in another collection · chain A against A, TM-score 1.00
O94953 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 4B (O94953) · a predicted model of the same protein · chain A against A, TM-score 0.69

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 O94953
Elsewhere: RCSB PDB 4UC4 · PDBe 4UC4 · UniProt O94953

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