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Crystal structure of a 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine (MTA/SAH) nucleosidase (mtan) from colwellia psychrerythraea 34H (CPS_4743, target psi-029300) in complex with adenine at 2.27 a resolution

Analyse Crystal structure of a 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine (MTA/SAH)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5DK6
Type: protein
Length: 242 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase
EC: 3.2.2.9
UniProt: Q47UY5
Ligands: GLY, ADE
Pockets: 1 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9)	protein	242	34% helix, 29% strand	Q47UY5

Ligands and binding sites

GLY · Glycine · ligand · chains A
ADE · Adenine · ligand · chains A

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	86	0.63	0.90	20	GLY, ADE

Modifications

Observed in the structure: 7 modified (engineered).

Compared structures

5DK6 · Crystal structure of a 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine (MTA/SAH)… · the same entry in another collection · chain A against A, TM-score 1.00
Q47UY5 · AlphaFold monomer V2.0 prediction for 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q47UY5
Elsewhere: RCSB PDB 5DK6 · PDBe 5DK6 · UniProt Q47UY5

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