Research workbench

Delta-N METTL16 mtase domain

Analyse Delta-N METTL16 mtase domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GFK
Type: protein
Length: 668 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
EC: 2.1.1.346, 2.1.1.62
UniProt: Q86W50
Ligands: SAH, SO4
Pockets: 8 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase (EC 2.1.1.346, 2.1.1.62)	protein	230	42% helix, 21% strand	Q86W50
B	U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase (EC 2.1.1.346, 2.1.1.62)	protein	220	39% helix, 22% strand	Q86W50
C	U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase (EC 2.1.1.346, 2.1.1.62)	protein	218	39% helix, 22% strand	Q86W50

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 5 copies · chains A, B, C

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

Pockets

8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	858	0.74	0.78	84	empty
2	323	0.66	0.81	41	SAH, SO4
3	52	0.65	0.95	17	empty
4	281	0.62	0.80	38	SAH, SO4
5	272	0.60	0.79	40	SAH, SO4

Interfaces

3 interfaces between chains.

A–C · 919 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 423 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 303 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6GFK · delta-N METTL16 MTase domain · the same entry in another collection · chain A against A, TM-score 1.00
Q86W50 · AlphaFold monomer V2.0 prediction for RNA N6-adenosine- methyltransferase METTL16 (Q86W50) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 Q86W50
Elsewhere: RCSB PDB 6GFK · PDBe 6GFK · UniProt Q86W50

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