MolNFT v1 · #108866 · protein
Crystal structure of helicobacter pylori 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan) complexed with hydroxybutylthio-dadme-immucillin-a
4WKO · Aminodeoxyfutalosine nucleosidase: “Crystal structure of helicobacter pylori 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan)…”. X-ray diffraction, 1 ligand (GMD), 1 pocket (best druggability 0.65). MolNFT v1…
- PDB
- 4WKO
- Type
- protein
- Length
- 230 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminodeoxyfutalosine nucleosidase
- EC
- 3.2.2.9
- UniProt
- Q9ZMY2
- Ligands
- GMD
- Pockets
- 1 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminodeoxyfutalosine nucleosidase (EC 3.2.2.9) | protein | 230 | 39% helix, 31% strand | Q9ZMY2 |
Ligands and binding sites
- GMD · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-hydroxybutyl)sulfanyl]methyl}pyrrolidin-3-ol · ligand · 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 | 89 | 0.65 | 0.90 | 19 | GMD |
Compared structures
- 4WKO · 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 4WKO · PDBe 4WKO · UniProt Q9ZMY2
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