MolNFT v1 · #3764 · protein

Crystal structure of R175K mutant glycine N-methyltransferase from rat liver

1D2G: “Crystal structure of R175K mutant glycine N-methyltransferase from rat liver”. X-ray diffraction, 7 pockets (best druggability 0.83). MolNFT v1 #3764 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1D2G
Type: protein
Length: 584 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycine N-methyltransferase
EC: 2.1.1.20
UniProt: P13255
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glycine N-methyltransferase (EC 2.1.1.20)	protein	292	30% helix, 28% strand	P13255

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	271	0.83	0.94	41	empty
2	286	0.82	0.92	43	empty
3	404	0.78	0.87	49	empty
4	124	0.43	0.76	24	empty
5	115	0.42	0.77	24	empty

Interfaces

1 interface between chains.

A–B · 2414 Å² buried · 42 hydrogen bonds · protein-protein

Compared structures

1D2G · Crystal structure of R175K mutant glycine N-methyltransferase from rat liver · the same entry in another collection · chain A against A, TM-score 1.00
P13255 · AlphaFold monomer V2.0 prediction for glycine N-methyltransferase (P13255) · a predicted model of the same protein · chain A against A, TM-score 0.88

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 P13255
Elsewhere: RCSB PDB 1D2G · PDBe 1D2G · UniProt P13255

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