MolNFT v1 · #92322 · protein

Crystal structure of S-adenosylhomocysteine nucleosidase from streptococcus pyogenes in complex with 5-methylthiotubericidin

4G41 · MTA/SAH nucleosidase: “Crystal structure of S-adenosylhomocysteine nucleosidase from streptococcus pyogenes in complex with…”. X-ray diffraction, 1 ligand (MTA), 4 pockets (best druggability 0.67). MolNFT v1 #92322 on GenesisL1: 3D…

PDB: 4G41
Type: protein
Length: 472 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: E0PXI9
Ligands: MTA
Pockets: 4 · best druggability 0.67

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	MTA/SAH nucleosidase (EC 3.2.2.16, 3.2.2.9)	protein	236	34% helix, 29% strand	E0PXI9

Ligands and binding sites

MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 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	100	0.67	0.91	24	MTA
2	352	0.64	0.79	43	empty
3	226	0.52	0.76	22	empty
4	56	0.42	0.82	19	empty

Interfaces

1 interface between chains.

A–B · 1550 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4G41 · Crystal structure of s-adenosylhomocysteine nucleosidase from streptococcus pyogenes in… · 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 E0PXI9
Elsewhere: RCSB PDB 4G41 · PDBe 4G41 · UniProt E0PXI9

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