MolNFT v1 · #189219 · protein

Lccomt in complex with SAM

7V6J: “Lccomt in complex with SAM”. X-ray diffraction, 2 ligands (SAM, NA), 9 pockets (best druggability 0.78). MolNFT v1 #189219 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7V6J
Type: protein
Length: 687 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lccomt
Ligands: SAM, NA
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lccomt	protein	346	51% helix, 16% strand	—
B	Lccomt	protein	341	49% helix, 17% strand	—

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · chains A, B

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

Pockets

9 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	921	0.78	0.80	64	SAM
2	870	0.78	0.81	63	SAM
3	185	0.57	0.80	19	empty
4	159	0.45	0.76	33	empty
5	131	0.41	0.75	26	empty

Interfaces

1 interface between chains.

A–B · 4441 Å² buried · 48 hydrogen bonds · protein-protein

Compared structures

7V6J · LcCOMT in complex with 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
Elsewhere: RCSB PDB 7V6J · PDBe 7V6J

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