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Crystal structure and mechanism of human lysine-specific demethylase-1

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

PDB: 2H94
Type: protein
Length: 647 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: FAD, HG
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific histone demethylase 1 (EC 1.-.-.-)	protein	647	42% helix, 15% strand	O60341

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · chains A
HG · Mercury (II) ion · metal · 3 copies · 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	1000	0.82	0.83	93	HG, FAD
2	295	0.58	0.77	28	empty
3	90	0.43	0.79	18	empty
4	135	0.41	0.75	22	empty
5	53	0.30	0.76	14	empty

Compared structures

2H94 · Crystal Structure and Mechanism of human Lysine-Specific 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 2H94 · PDBe 2H94 · UniProt O60341

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