Research workbench

Human nicotinamide N-methyltransferase

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

PDB: 2IIP
Type: protein
Length: 1,031 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
Pockets: 10 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nicotinamide N-methyltransferase (EC 2.1.1.1)	protein	265	36% helix, 25% strand	P40261
B	Nicotinamide N-methyltransferase (EC 2.1.1.1)	protein	264	37% helix, 25% strand	P40261
C	Nicotinamide N-methyltransferase (EC 2.1.1.1)	protein	251	39% helix, 26% strand	P40261
D	Nicotinamide N-methyltransferase (EC 2.1.1.1)	protein	251	39% helix, 26% strand	P40261

Ligands and binding sites

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

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	200	0.79	0.93	40	SAH
2	225	0.78	0.92	44	SAH
3	645	0.76	0.82	87	SAH
4	145	0.75	0.93	31	SAH
5	324	0.61	0.78	46	empty

Interfaces

4 interfaces between chains.

A–B · 660 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 490 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 459 Å² buried · 1 hydrogen bond · protein-protein
B–C · 456 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2IIP · Human Nicotinamide N-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 2IIP · PDBe 2IIP · UniProt P40261

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