MolNFT v1 · #84511 · protein

LSD1-corest in complex with prsfav peptide

3ZMZ · Lysine-specific histone demethylase 1A: “LSD1-corest in complex with prsfav peptide”. X-ray diffraction, 1 ligand (FAD), 9 pockets (best druggability 0.85). MolNFT v1 #84511 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3ZMZ
Type: protein
Length: 805 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific histone demethylase 1A; Rest corepressor 1; Peptide
EC: 1.-.-.-
UniProt: O60341, Q9UKL0
Ligands: FAD
Pockets: 9 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 14% 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	133	63% helix, 0% strand	Q9UKL0
C	Peptide	protein	6	50% helix, 0% strand	—

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · chains A, C

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

Pockets

9 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	323	0.85	0.95	56	FAD
2	373	0.62	0.77	34	empty
3	224	0.52	0.76	27	empty
4	96	0.47	0.80	19	empty
5	95	0.42	0.78	24	empty

Interfaces

2 interfaces between chains.

A–B · 2787 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 613 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3ZMZ · LSD1-CoREST in complex with PRSFAV peptide · 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 0.97

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 3ZMZ · PDBe 3ZMZ · UniProt O60341 · UniProt Q9UKL0

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