Research workbench
Crystal structure of helicobacter pylori 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan) complexed with (((4-amino- 5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL)(HEXYL)AMINO)METHANOL
Analyse Crystal structure of helicobacter pylori 5'-METHYLTHIOADENOSINE/S- adenosyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YO8
- Type
- protein
- Length
- 480 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminodeoxyfutalosine nucleosidase
- EC
- 3.2.2.30, 3.2.2.9
- UniProt
- Q9ZMY2
- Ligands
- 4EZ, ZN
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminodeoxyfutalosine nucleosidase (EC 3.2.2.30, 3.2.2.9) | protein | 238 | 38% helix, 29% strand | Q9ZMY2 |
| B | Aminodeoxyfutalosine nucleosidase (EC 3.2.2.30, 3.2.2.9) | protein | 242 | 38% helix, 29% strand | Q9ZMY2 |
Ligands and binding sites
- 4EZ · {[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl](hexyl)amino}methanol · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.71 | 0.89 | 30 | 4EZ |
| 2 | 143 | 0.70 | 0.90 | 26 | 4EZ |
| 3 | 154 | 0.42 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1661 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4YO8 · Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ZMY2 · AlphaFold monomer V2.0 prediction for aminodeoxyfutalosine nucleosidase (Q9ZMY2) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9ZMY2
- Elsewhere: RCSB PDB 4YO8 · PDBe 4YO8 · UniProt Q9ZMY2
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