MolNFT v1 · #123245 · protein

Crystal structure of burkholderia glumae toxa Y7A mutant with bound S- adenosylhomocysteine (sah)

5JE3 · Methyl transferase: “Crystal structure of burkholderia glumae toxa Y7A mutant with bound S- adenosylhomocysteine (sah)”. X-ray diffraction, 1 ligand (SAH), 3 pockets (best druggability 0.75). MolNFT v1 #123245 on GenesisL1: 3D…

PDB: 5JE3
Type: protein
Length: 439 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methyl transferase
UniProt: Q9LBJ0
Ligands: SAH
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methyl transferase	protein	220	35% helix, 30% strand	Q9LBJ0
B	Methyl transferase	protein	219	36% helix, 30% strand	Q9LBJ0

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

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	903	0.75	0.78	107	SAH
2	142	0.46	0.77	16	empty
3	153	0.46	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 621 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5JE3 · Crystal structure of Burkholderia glumae ToxA Y7A mutant with bound… · 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 Q9LBJ0
Elsewhere: RCSB PDB 5JE3 · PDBe 5JE3 · UniProt Q9LBJ0

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