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Crystal structure of SAM-dependent methyltransferase from thiobacillus denitrificans in complex with S-adenosyl-L-homocysteine

Analyse Crystal structure of SAM-dependent methyltransferase from thiobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EPE
Type: protein
Length: 248 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SAM-dependent methyltransferase
EC: 2.1.1.-
UniProt: Q3SJX0
Ligands: SAH, NA
Pockets: 2 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SAM-dependent methyltransferase (EC 2.1.1.-)	protein	248	47% helix, 23% strand	Q3SJX0

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · chains A
NA · Sodium ion · metal · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	590	0.73	0.80	58	SAH
2	50	0.28	0.75	12	empty

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

5EPE · Crystal structure of SAM-dependent methyltransferase from Thiobacillus denitrificans in… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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Every structure of UniProt Q3SJX0
Elsewhere: RCSB PDB 5EPE · PDBe 5EPE · UniProt Q3SJX0

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