MolNFT v1 · #125247 · protein

Human LSD1/COREST: LSD1 E379K mutation

5L3C · Lysine-specific histone demethylase 1A: “Human LSD1/COREST: LSD1 E379K mutation”. X-ray diffraction, 1 ligand (FAD), 8 pockets (best druggability 0.82). MolNFT v1 #125247 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5L3C
Type: protein
Length: 800 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific histone demethylase 1A; Rest corepressor 1
EC: 1.-.-.-
UniProt: O60341, Q9UKL0
Ligands: FAD
Pockets: 8 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific histone demethylase 1A (EC 1.-.-.-)	protein	666	45% helix, 16% strand	O60341
B	Rest corepressor 1	protein	134	65% helix, 0% strand	Q9UKL0

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · chains A

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1051	0.82	0.83	90	FAD
2	314	0.60	0.78	27	empty
3	246	0.50	0.75	29	empty
4	87	0.45	0.80	19	empty
5	101	0.42	0.78	23	empty

Interfaces

1 interface between chains.

A–B · 2736 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

5L3C · Human LSD1/CoREST: LSD1 E379K mutation · the same entry in another collection · chain A against A, TM-score 1.00
Q9UKL0 · AlphaFold monomer V2.0 prediction for rest corepressor 1 (Q9UKL0) · a predicted model of the same protein · chain B against A, TM-score 0.96

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
Every structure of UniProt Q9UKL0
Elsewhere: RCSB PDB 5L3C · PDBe 5L3C · UniProt O60341 · UniProt Q9UKL0

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