MolNFT v1 · #114816 · protein

Crystal structure of JARID1A phd finger bound to histone H3C4ME3 peptide

5C11 · Lysine-specific demethylase 5A: “Crystal structure of JARID1A phd finger bound to histone H3C4ME3 peptide”. X-ray diffraction, 1 ligand (ZN). MolNFT v1 #114816 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5C11
Type: protein
Length: 59 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific demethylase 5A; H3 peptide
EC: 1.14.11.-
UniProt: P29375
Ligands: ZN

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific demethylase 5A (EC 1.14.11.-)	protein	52	19% helix, 15% strand	P29375
B	H3 peptide	protein	7	0% helix, 57% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A

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

Interfaces

1 interface between chains.

A–B · 556 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (nonstandard).

Compared structures

5C11 · Crystal Structure of Jarid1a PHD finger bound to histone H3C4me3 peptide · the same entry in another collection · chain A against A, TM-score 1.00
P29375 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5A (P29375) · a predicted model of the same protein · chain A against A, TM-score 0.91

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 P29375
Elsewhere: RCSB PDB 5C11 · PDBe 5C11 · UniProt P29375

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