MolNFT v1 · #114276 · protein

Structures and functional analysis of periplasmic 5- METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase from aeromonas hydrophila

5B7P · MTA/SAH nucleosidase: “Structures and functional analysis of periplasmic 5- METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase…”. X-ray diffraction, 1 ligand (MTA), 2 pockets (best druggability 0.66). MolNFT v1 #114276 on…

PDB: 5B7P
Type: protein
Length: 495 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: MTA
Pockets: 2 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MTA/SAH nucleosidase (EC 3.2.2.16, 3.2.2.9)	protein	248	35% helix, 34% strand	A0KGU9
B	MTA/SAH nucleosidase (EC 3.2.2.16, 3.2.2.9)	protein	247	35% helix, 34% strand	A0KGU9

Ligands and binding sites

MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 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	122	0.66	0.89	25	MTA
2	100	0.61	0.87	19	MTA

Interfaces

1 interface between chains.

A–B · 2540 Å² buried · 38 hydrogen bonds · protein-protein

Compared structures

5B7P · Structures and functional analysis of periplasmic… · 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 5B7P · PDBe 5B7P · UniProt A0KGU9

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