Research workbench
Crystal structure of periplasmic 5-METHYLTHIOADENOSINE/S- adenosylhomocysteine nucleosidase from aeromonas hydrophila
Analyse Crystal structure of periplasmic 5-METHYLTHIOADENOSINE/S- adenosylhomocysteine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B7N
- Type
- protein
- Length
- 496 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
- A0KGU9
- Ligands
- SAH
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | MTA/SAH nucleosidase (EC 3.2.2.16, 3.2.2.9) | protein | 248 | 35% helix, 35% strand | A0KGU9 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.60 | 0.86 | 20 | SAH |
| 2 | 111 | 0.57 | 0.85 | 20 | SAH |
Interfaces
1 interface between chains.
- A–B · 2520 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 5B7N · Crystal structure of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine… · 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 A0KGU9
- Elsewhere: RCSB PDB 5B7N · PDBe 5B7N · UniProt A0KGU9
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