MolNFT v1 · #128601 · protein

Human DNMT3B pwwp domain in complex with choline

5NVO · DNA (cytosine-5)-methyltransferase 3B: “Human DNMT3B pwwp domain in complex with choline”. X-ray diffraction, 2 ligands (CHT, SO4), 2 pockets (best druggability 0.59). MolNFT v1 #128601 on GenesisL1: 3D structure, binding sites and…

PDB: 5NVO
Type: protein
Length: 256 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (cytosine-5)-methyltransferase 3B
EC: 2.1.1.37
UniProt: Q9UBC3
Ligands: CHT, SO4
Pockets: 2 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37)	protein	128	34% helix, 19% strand	Q9UBC3

Ligands and binding sites

CHT · Choline ion · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 9 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	349	0.59	0.76	43	SO4
2	58	0.35	0.78	14	empty

Interfaces

1 interface between chains.

A–B · 495 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5NVO · Human DNMT3B PWWP domain in complex with choline · the same entry in another collection · chain A against A, TM-score 1.00
Q9UBC3 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3B (Q9UBC3) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q9UBC3
Elsewhere: RCSB PDB 5NVO · PDBe 5NVO · UniProt Q9UBC3

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