MolNFT v1 · #108867 · protein
Crystal structure of helicobacter pylori 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan) complexed with 2-(2- HYDROXYETHOXY)ETHYLTHIOMETHYL-dadme-immucillin-a
4WKP · Aminodeoxyfutalosine nucleosidase: “Crystal structure of helicobacter pylori 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan)…”. X-ray diffraction, 2 ligands (3QA, SO4), 8 pockets (best druggability 0.72). MolNFT…
- PDB
- 4WKP
- Type
- protein
- Length
- 920 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminodeoxyfutalosine nucleosidase
- EC
- 3.2.2.9
- UniProt
- Q9ZMY2
- Ligands
- 3QA, SO4
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Aminodeoxyfutalosine nucleosidase (EC 3.2.2.9) | protein | 230 | 39% helix, 31% strand | Q9ZMY2 |
Ligands and binding sites
- 3QA · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-(2-{[2-(2-hydroxyethoxy)ethyl]sulfanyl}ethyl)pyrrolidin-3-ol · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.72 | 0.91 | 24 | 3QA |
| 2 | 471 | 0.70 | 0.80 | 53 | 3QA |
| 3 | 163 | 0.70 | 0.88 | 29 | 3QA |
| 4 | 158 | 0.70 | 0.88 | 31 | 3QA |
| 5 | 79 | 0.45 | 0.81 | 15 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1717 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1685 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 280 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 170 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4WKP · 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 4WKP · PDBe 4WKP · UniProt Q9ZMY2
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