MolNFT v1 · #123241 · protein

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

5JDZ · Methyl transferase: “Crystal structure of burkholderia glumae toxa with bound S- adenosylhomocysteine (sah)”. X-ray diffraction, 1 ligand (SAH), 4 pockets (best druggability 0.70). MolNFT v1 #123241 on GenesisL1: 3D structure…

PDB: 5JDZ
Type: protein
Length: 459 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methyl transferase
UniProt: Q9LBJ0
Ligands: SAH
Pockets: 4 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methyl transferase	protein	239	36% helix, 28% strand	Q9LBJ0
B	Methyl transferase	protein	220	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

4 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	637	0.70	0.78	75	SAH
2	247	0.69	0.85	46	SAH
3	183	0.58	0.81	26	empty
4	161	0.45	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 664 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5JDZ · Crystal structure of Burkholderia glumae ToxA with bound S-adenosylhomocysteine (SAH) · the same entry in another collection · chain B against B, 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 5JDZ · PDBe 5JDZ · UniProt Q9LBJ0

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