MolNFT v1 · #114275 · protein

Crystal structure of periplasmic 5-METHYLTHIOADENOSINE/S- adenosylhomocysteine nucleosidase from aeromonas hydrophila

5B7N · MTA/SAH nucleosidase: “Crystal structure of periplasmic 5-METHYLTHIOADENOSINE/S- adenosylhomocysteine nucleosidase from aeromonas…”. X-ray diffraction, 1 ligand (SAH), 2 pockets (best druggability 0.60). MolNFT v1 #114275 on…

PDB: 5B7N
Type: protein
Length: 496 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MTA/SAH nucleosidase
EC: 3.2.2.16, 3.2.2.9
UniProt: A0KGU9
Ligands: SAH
Pockets: 2 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	MTA/SAH nucleosidase (EC 3.2.2.16, 3.2.2.9)	protein	248	35% helix, 35% strand	A0KGU9

Ligands and binding sites

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

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	107	0.60	0.86	20	SAH
2	111	0.57	0.85	20	SAH

Interfaces

1 interface between chains.

A–B · 2520 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

5B7N · Crystal structure of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine… · 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 A0KGU9
Elsewhere: RCSB PDB 5B7N · PDBe 5B7N · UniProt A0KGU9

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