GL1X · GenesisL1 explorer

MolNFT v1 · #59893 · protein

SET7/9-er-adomet complex

3CBM · Histone-lysine N-methyltransferase SETD7: “SET7/9-er-adomet complex”. X-ray diffraction, 1 ligand (SAH), 2 pockets (best druggability 0.45). MolNFT v1 #59893 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
3CBM
Type
protein
Length
250 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Histone-lysine N-methyltransferase SETD7; Estrogen receptor
EC
2.1.1.43
UniProt
Q8WTS6
Ligands
SAH
Pockets
2 · best druggability 0.45

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 38% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AHistone-lysine N-methyltransferase SETD7 (EC 2.1.1.43)protein24311% helix, 39% strandQ8WTS6
BEstrogen receptorprotein70% helix, 14% strand—

Ligands and binding sites

  • SAH · S-adenosyl-L-homocysteine · ligand · chains A, B
  • BME · Beta-mercaptoethanol · additive · 3 copies · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11620.450.7522SAH
2550.330.7716empty

Interfaces

1 interface between chains.

  • A–B · 742 Ų buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 1 modified (additive adduct, methylation).

Compared structures

  • 3CBM · SET7/9-ER-AdoMet complex · the same entry in another collection · chain A against A, TM-score 1.00
  • Q8WTS6 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SETD7 (Q8WTS6) · a predicted model of the same protein · chain A against A, TM-score 0.99

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