Research workbench
Crystal structure of S-adenosylhomocysteine nucleosidase from streptococcus pyogenes in complex with 5-methylthiotubericidin
Analyse Crystal structure of S-adenosylhomocysteine nucleosidase from streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų 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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