Research workbench

Methyltransferase

Analyse Methyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ROD
Type: protein
Length: 1,034 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nicotinamide N-methyltransferase
EC: 2.1.1.1
UniProt: P40261
Ligands: SAH, NCA
Pockets: 12 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Nicotinamide N-methyltransferase (EC 2.1.1.1)	protein	259	37% helix, 25% strand	P40261
D	Nicotinamide N-methyltransferase (EC 2.1.1.1)	protein	257	37% helix, 24% strand	P40261

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
NCA · Nicotinamide · ligand · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	195	0.82	0.96	40	SAH, NCA
2	220	0.81	0.94	43	SAH, NCA
3	203	0.80	0.94	41	SAH, NCA
4	404	0.77	0.86	64	empty
5	409	0.77	0.86	47	empty

Interfaces

5 interfaces between chains.

A–B · 805 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 750 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 359 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 275 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 268 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3ROD · Methyltransferase · the same entry in another collection · chain D against D, TM-score 1.00
P40261 · AlphaFold monomer V2.0 prediction for nicotinamide N-methyltransferase (P40261) · a predicted model of the same protein · chain D 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 P40261
Elsewhere: RCSB PDB 3ROD · PDBe 3ROD · UniProt P40261

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