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Structure of the alpha-N-methyltransferase (sonm mutant R67A) and ripp precursor (sona) heteromeric complex (with sah)

Analyse Structure of the alpha-N-methyltransferase (sonm mutant R67A) and ripp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7LTS
Type: protein
Length: 667 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tp-methylase family protein; Liga domain-containing protein
UniProt: Q8EGW3, Q8EGW2
Ligands: SAH
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Tp-methylase family protein	protein	262	37% helix, 21% strand	Q8EGW3
B	Liga domain-containing protein	protein	71	68% helix, 1% strand	Q8EGW2
D	Liga domain-containing protein	protein	72	67% helix, 0% strand	Q8EGW2

Ligands and binding sites

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

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

Pockets

6 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	340	0.79	0.89	53	SAH
2	524	0.78	0.85	70	SAH
3	342	0.65	0.80	49	empty
4	245	0.61	0.81	38	empty
5	160	0.45	0.75	26	empty

Interfaces

5 interfaces between chains.

A–C · 2804 Å² buried · 41 hydrogen bonds · protein-protein
C–D · 1710 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1619 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 765 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 735 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7LTS · Structure of the alpha-N-methyltransferase (SonM mutant R67A) and RiPP precursor (SonA)… · 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 Q8EGW3
Every structure of UniProt Q8EGW2
Elsewhere: RCSB PDB 7LTS · PDBe 7LTS · UniProt Q8EGW3 · UniProt Q8EGW2

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