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Structure of methyltransferase domain of SPB1 boudn to SAM

Analyse Structure of methyltransferase domain of SPB1 boudn to SAM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7R7O
Type: protein
Length: 418 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adomet-dependent rRNA methyltransferase SPB1
EC: 2.1.1.-
UniProt: A0A7I9D0Y8
Ligands: SAM
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Adomet-dependent rRNA methyltransferase SPB1 (EC 2.1.1.-)	protein	209	41% helix, 24% strand	A0A7I9D0Y8

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B

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	350	0.57	0.75	39	empty
2	176	0.47	0.76	36	SAM
3	163	0.45	0.76	34	SAM

Interfaces

1 interface between chains.

A–B · 95 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

7R7O · Structure of methyltransferase domain of Spb1 boudn to SAM · 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 A0A7I9D0Y8
Elsewhere: RCSB PDB 7R7O · PDBe 7R7O · UniProt A0A7I9D0Y8

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