Research workbench

Guanidinoacetate methyltransferase

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

PDB: 1P1B
Type: protein
Length: 772 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanidinoacetate N-methyltransferase
EC: 2.1.1.2
UniProt: P10868
Ligands: SAH
Pockets: 4 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Guanidinoacetate N-methyltransferase (EC 2.1.1.2)	protein	193	37% helix, 26% strand	P10868

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

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	990	0.82	0.83	97	SAH
2	791	0.81	0.84	96	SAH
3	124	0.47	0.78	23	empty
4	123	0.40	0.75	20	empty

Interfaces

4 interfaces between chains.

A–B · 1215 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1079 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 393 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 113 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1P1B · Guanidinoacetate methyltransferase · the same entry in another collection · chain A against A, TM-score 1.00
P10868 · AlphaFold monomer V2.0 prediction for guanidinoacetate N-methyltransferase (P10868) · a predicted model of the same protein · chain B 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 P10868
Elsewhere: RCSB PDB 1P1B · PDBe 1P1B · UniProt P10868

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