MolNFT v1 · #29961 · protein

Structure of 5'-METHYLTHIONADENOSINE/S-adenosylhomocysteine nucleosidase from S. pneumoniae with a transition-state inhibitor mt- imma

1ZOS · 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase: “Structure of 5'-METHYLTHIONADENOSINE/S-adenosylhomocysteine nucleosidase from S. pneumoniae with a…”. X-ray diffraction, 1 ligand (MTM), 19 pockets (best druggability…

PDB: 1ZOS
Type: protein
Length: 1,380 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase
EC: 3.2.2.16
UniProt: Q8DQ16
Ligands: MTM
Pockets: 19 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	5'-methylthioadenosine / S-adenosylhomocysteine nucleosidase (EC 3.2.2.16)	protein	230	36% helix, 32% strand	Q8DQ16

Ligands and binding sites

MTM · (3S,4R)-2-(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)-5-[(methylsulfanyl)methyl]pyrrolidine-3,4-diol · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	119	0.71	0.92	26	MTM
2	113	0.71	0.92	26	MTM
3	116	0.70	0.91	25	MTM
4	126	0.70	0.91	26	MTM
5	122	0.70	0.91	25	MTM

Interfaces

7 interfaces between chains.

A–B · 1664 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1664 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 1657 Å² buried · 10 hydrogen bonds · protein-protein
A–F · 578 Å² buried · 9 hydrogen bonds · protein-protein
C–F · 565 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

1ZOS · Structure of 5'-methylthionadenosine/S-Adenosylhomocysteine nucleosidase from S.… · 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 Q8DQ16
Elsewhere: RCSB PDB 1ZOS · PDBe 1ZOS · UniProt Q8DQ16

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