MolNFT v1 · #181398 · protein

Structure of the heteromeric complex between the alpha-N- methyltransferase (sonm) and a truncated construct of the ripp precursor (sona) (with SAM)

7LTR · Tp-methylase family protein: “Structure of the heteromeric complex between the alpha-N- methyltransferase (sonm) and a truncated construct…”. X-ray diffraction, 1 ligand (SAM), 8 pockets (best druggability 0.85). MolNFT v1 #181398…

PDB: 7LTR
Type: protein
Length: 1,252 residues
Chains: 8
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: SAM
Pockets: 8 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 46% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tp-methylase family protein	protein	261	38% helix, 21% strand	Q8EGW3
B	Liga domain-containing protein	protein	51	78% helix, 0% strand	Q8EGW2
C, H, J	Tp-methylase family protein	protein	262	37% helix, 21% strand	Q8EGW3
D, K	Liga domain-containing protein	protein	51	78% helix, 0% strand	Q8EGW2
I	Liga domain-containing protein	protein	52	73% helix, 0% strand	Q8EGW2

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A, H
GOL · Glycerol · additive · 4 copies · chains A, C, H, J

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

Pockets

8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1017	0.85	0.86	111	empty
2	762	0.78	0.82	63	SAM, GOL
3	862	0.78	0.80	69	SAM, GOL
4	405	0.74	0.84	53	GOL
5	570	0.73	0.81	69	GOL

Interfaces

14 interfaces between chains.

A–C · 2865 Å² buried · 52 hydrogen bonds · protein-protein
H–J · 2858 Å² buried · 48 hydrogen bonds · protein-protein
H–I · 650 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 637 Å² buried · 1 hydrogen bond · protein-protein
C–D · 621 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7LTR · Structure of the heteromeric complex between the alpha-N-methyltransferase (SonM) and a… · 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 7LTR · PDBe 7LTR · UniProt Q8EGW3 · UniProt Q8EGW2

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