MolNFT v1 · #61468 · protein

T. thermophilus 16S rRNA N2 G1207 methyltransferase (rsmc) in complex with adomet and guanosine

3DMH · Probable ribosomal RNA small subunit methyltransferase: “T. thermophilus 16S rRNA N2 G1207 methyltransferase (rsmc) in complex with adomet and guanosine”. X-ray diffraction, 3 ligands (SAM, GMP, SO4), 3 pockets (best druggability…

PDB: 3DMH
Type: protein
Length: 371 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable ribosomal RNA small subunit methyltransferase
EC: 2.1.1.-
UniProt: Q5SKW0
Ligands: SAM, GMP, SO4
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable ribosomal RNA small subunit methyltransferase (EC 2.1.1.-)	protein	371	31% helix, 31% strand	Q5SKW0

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · chains A
GMP · Guanosine · ligand · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A

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

Pockets

3 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	606	0.72	0.80	62	SO4, SAM
2	60	0.39	0.79	11	empty
3	56	0.36	0.79	18	GMP

Compared structures

3DMH · T. Thermophilus 16S rRNA N2 G1207 methyltransferase (RsmC) in complex with AdoMet and… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q5SKW0
Elsewhere: RCSB PDB 3DMH · PDBe 3DMH · UniProt Q5SKW0

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