MolNFT v1 · #134731 · protein

SET3 phd finger in complex with histone H3K4ME2

5TDR · Set domain-containing protein 3: “SET3 phd finger in complex with histone H3K4ME2”. X-ray diffraction, 2 ligands (ZN, NA). MolNFT v1 #134731 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5TDR
Type: protein
Length: 81 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Set domain-containing protein 3; Histone H3
UniProt: P36124
Ligands: ZN, NA

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Set domain-containing protein 3	protein	70	30% helix, 11% strand	P36124
B	Histone H3	protein	11	0% helix, 36% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A
NA · Sodium 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 · 528 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (methylation).

Compared structures

5TDR · Set3 PHD finger in complex with histone H3K4me2 · the same entry in another collection · chain A against A, TM-score 1.00
P36124 · AlphaFold monomer V2.0 prediction for set domain-containing protein 3 (P36124) · a predicted model of the same protein · chain A 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 P36124
Elsewhere: RCSB PDB 5TDR · PDBe 5TDR · UniProt P36124

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.