Research workbench

RV2258C-SAH

Analyse RV2258C-SAH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5F8E
Type: protein
Length: 1,058 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methyltransferase
UniProt: O53532
Ligands: SAH
Pockets: 10 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methyltransferase	protein	353	54% helix, 15% strand	O53532
B	Methyltransferase	protein	350	51% helix, 17% strand	O53532
C	Methyltransferase	protein	355	51% helix, 16% strand	O53532

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1017	0.83	0.84	84	empty
2	784	0.83	0.86	97	SAH
3	1015	0.80	0.81	91	SAH
4	228	0.52	0.76	39	empty
5	131	0.45	0.77	24	empty

Interfaces

2 interfaces between chains.

A–B · 3821 Å² buried · 52 hydrogen bonds · protein-protein
B–C · 869 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (oxidation).

Compared structures

5F8E · Rv2258c-SAH · the same entry in another collection · chain A against A, TM-score 1.00
O53532 · AlphaFold monomer V2.0 prediction for uncharacterized S-adenosylmethionine-dependent… · a predicted model of the same protein · chain B against A, TM-score 0.98

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 O53532
Elsewhere: RCSB PDB 5F8E · PDBe 5F8E · UniProt O53532

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