MolNFT v1 · #111318 · protein
Crystal structure of helicobacter pylori 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan) complexed with pyrazinylthio-dadme-immucillin-a
4YNB · Aminodeoxyfutalosine nucleosidase: “Crystal structure of helicobacter pylori 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan)…”. X-ray diffraction, 1 ligand (4EH), 1 pocket (best druggability 0.62). MolNFT v1…
- PDB
- 4YNB
- Type
- protein
- Length
- 230 residues
- Chains
- 1
- 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
- 4EH
- Pockets
- 1 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminodeoxyfutalosine nucleosidase (EC 3.2.2.30, 3.2.2.9) | protein | 230 | 37% helix, 30% strand | Q9ZMY2 |
Ligands and binding sites
- 4EH · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl) methyl]-4-[(pyrazin-2-ylsulfanyl)methyl]pyrrolidin-3-ol · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.62 | 0.89 | 19 | 4EH |
Compared structures
- 4YNB · 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 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 Q9ZMY2
- Elsewhere: RCSB PDB 4YNB · PDBe 4YNB · UniProt Q9ZMY2
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