Research workbench

Helicobacter pylori mtan complexed with adenine and tris

Analyse Helicobacter pylori mtan complexed with adenine and tris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NM6
Type: protein
Length: 229 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MTA/SAH nucleosidase
EC: 3.2.2.9
UniProt: Q9ZMY2
Ligands: ADE
Pockets: 1 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	MTA/SAH nucleosidase (EC 3.2.2.9)	protein	229	38% helix, 30% strand	Q9ZMY2

Ligands and binding sites

ADE · Adenine · ligand · chains B
EDO · 1,2-ethanediol · additive · 4 copies · chains B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	72	0.64	0.91	19	ADE, TRS

Compared structures

3NM6 · Helicobacter pylori MTAN complexed with adenine and tris · the same entry in another collection · chain B against B, TM-score 1.00
Q9ZMY2 · AlphaFold monomer V2.0 prediction for aminodeoxyfutalosine nucleosidase (Q9ZMY2) · a predicted model of the same protein · chain B 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 Q9ZMY2
Elsewhere: RCSB PDB 3NM6 · PDBe 3NM6 · UniProt Q9ZMY2

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