MolNFT v1 · #20252 · protein

Crystal structure of mouse glycine N-methyltransferase (monoclinic form)

1R8Y: “Crystal structure of mouse glycine N-methyltransferase (monoclinic form)”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #20252 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1R8Y
Type: protein
Length: 2,265 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycine N-methyltransferase
UniProt: Q9QXF8
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 7 distinct chains · 32% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycine N-methyltransferase	protein	281	32% helix, 27% strand	Q9QXF8
B, H	Glycine N-methyltransferase	protein	282	32% helix, 28% strand	Q9QXF8
C	Glycine N-methyltransferase	protein	283	32% helix, 27% strand	Q9QXF8
D	Glycine N-methyltransferase	protein	286	31% helix, 28% strand	Q9QXF8
E	Glycine N-methyltransferase	protein	286	30% helix, 27% strand	Q9QXF8
F	Glycine N-methyltransferase	protein	282	32% helix, 26% strand	Q9QXF8
G	Glycine N-methyltransferase	protein	283	32% helix, 28% strand	Q9QXF8

Ligands and binding sites

BME · Beta-mercaptoethanol · additive · 10 copies · chains A, B, D, E, F, G

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	404	0.84	0.92	68	empty
2	299	0.83	0.93	50	empty
3	263	0.82	0.94	43	empty
4	235	0.81	0.94	41	empty
5	437	0.80	0.88	66	empty

Interfaces

14 interfaces between chains.

G–H · 2366 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 2358 Å² buried · 46 hydrogen bonds · protein-protein
E–F · 2337 Å² buried · 42 hydrogen bonds · protein-protein
C–D · 2333 Å² buried · 40 hydrogen bonds · protein-protein
A–D · 1013 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 covalent (additive adduct).

Compared structures

1R8Y · Crystal Structure of Mouse Glycine N-Methyltransferase (Monoclinic Form) · the same entry in another collection · chain H against H, TM-score 1.00
Q9QXF8 · AlphaFold monomer V2.0 prediction for glycine N-methyltransferase (Q9QXF8) · a predicted model of the same protein · chain B against A, TM-score 0.89

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 Q9QXF8
Elsewhere: RCSB PDB 1R8Y · PDBe 1R8Y · UniProt Q9QXF8

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