MolNFT v1 · #152905 · protein

The structure of lepi C52A in complex with SAM and leporin C

6IX9 · O-methyltransferase lepi: “The structure of lepi C52A in complex with SAM and leporin C”. X-ray diffraction, 4 ligands (SAM, B0O, NA), 7 pockets (best druggability 0.86). MolNFT v1 #152905 on GenesisL1: 3D structure, binding sites…

PDB: 6IX9
Type: protein
Length: 778 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: O-methyltransferase lepi
EC: 2.1.1.-
UniProt: B8NJH3
Ligands: SAM, B0O, NA, CL
Pockets: 7 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	O-methyltransferase lepi (EC 2.1.1.-)	protein	389	53% helix, 13% strand	B8NJH3

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
B0O · (6R,6aS,10S,10aR)-10-methyl-4-phenyl-6-[(1E)-prop-1-en-1-yl]-2,6,6a,7,8,9,10,10a-octahydro-1H-[2]benzopyrano[4,3-c]pyridin-1-one · ligand · chains A, B
NA · Sodium ion · metal · chains A, B
CL · Chloride ion · ion · chains A, B
GOL · Glycerol · additive · chains B

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

Pockets

7 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	1178	0.86	0.86	92	SAM
2	1186	0.85	0.86	93	B0O, SAM, CL
3	308	0.66	0.82	38	NA
4	105	0.51	0.82	22	empty
5	163	0.49	0.78	20	empty

Interfaces

1 interface between chains.

A–B · 5133 Å² buried · 53 hydrogen bonds · protein-protein

Compared structures

6IX9 · The structure of LepI C52A in complex with SAM and leporin C · the same entry in another collection · chain A against A, TM-score 1.00
B8NJH3 · AlphaFold monomer V2.0 prediction for O-methyltransferase lepi (B8NJH3) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 B8NJH3
Elsewhere: RCSB PDB 6IX9 · PDBe 6IX9 · UniProt B8NJH3

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