Research workbench
Helicobacter pylori mtan complexed with formycin a
Analyse Helicobacter pylori mtan complexed with formycin a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NM5
- Type
- protein
- Length
- 458 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MTA/SAH nucleosidase
- EC
- 3.2.2.9
- UniProt
- Q9ZMY2
- Ligands
- FMC
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | MTA/SAH nucleosidase (EC 3.2.2.9) | protein | 229 | 39% helix, 30% strand | Q9ZMY2 |
Ligands and binding sites
- FMC · (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol · ligand · 2 copies · chains A, B
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 | 92 | 0.70 | 0.93 | 25 | FMC |
| 2 | 108 | 0.69 | 0.91 | 25 | FMC |
| 3 | 193 | 0.46 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1723 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
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 3NM5 · PDBe 3NM5 · UniProt Q9ZMY2
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