MolNFT v1 · #144924 · protein

Loganic acid methyltransferase with sah

6C8S · Loganic acid O-methyltransferase: “Loganic acid methyltransferase with sah”. X-ray diffraction, 1 ligand (SAH), 5 pockets (best druggability 0.86). MolNFT v1 #144924 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6C8S
Type: protein
Length: 708 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Loganic acid O-methyltransferase
UniProt: B2KPR3
Ligands: SAH
Pockets: 5 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Loganic acid O-methyltransferase	protein	354	45% helix, 16% strand	B2KPR3
B	Loganic acid O-methyltransferase	protein	354	45% helix, 16% strand	B2KPR3

Ligands and binding sites

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

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	539	0.86	0.92	67	SAH
2	714	0.84	0.87	80	SAH
3	189	0.54	0.79	25	empty
4	58	0.30	0.75	15	empty
5	52	0.29	0.76	20	empty

Interfaces

1 interface between chains.

A–B · 1123 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6C8S · Loganic acid methyltransferase with SAH · the same entry in another collection · chain A against A, TM-score 1.00
B2KPR3 · AlphaFold monomer V2.0 prediction for loganic acid O-methyltransferase (B2KPR3) · a predicted model of the same protein · chain B 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 B2KPR3
Elsewhere: RCSB PDB 6C8S · PDBe 6C8S · UniProt B2KPR3

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