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Crystal structure of lysine-specific histone demethylase 1

Analyse Crystal structure of lysine-specific histone demethylase 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Z5U
Type: protein
Length: 642 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific histone demethylase 1
EC: 1.-.-.-
UniProt: O60341
Ligands: FAJ
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific histone demethylase 1 (EC 1.-.-.-)	protein	642	44% helix, 17% strand	O60341

Ligands and binding sites

FAJ · FAD-trans-2-Phenylcyclopropylamine Adduct · ligand · chains A

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1022	0.82	0.83	92	FAJ
2	335	0.61	0.78	25	empty
3	102	0.44	0.78	17	empty
4	94	0.34	0.74	18	empty
5	62	0.28	0.73	11	empty

Compared structures

2Z5U · Crystal structure of Lysine-specific histone demethylase 1 · 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 O60341
Elsewhere: RCSB PDB 2Z5U · PDBe 2Z5U · UniProt O60341

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