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Crystal Structure of stachydrine demethylase in complex with cyanide, oxygen, and N-methyl proline in a new orientation
Analyse Crystal Structure of stachydrine demethylase in complex with cyanide, oxygen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QUR
- Type
- protein
- Length
- 415 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.759
- Source
- Sinorhizobium meliloti 1021
- Molecule
- monoxygenase; demethylase
- EC
- 1.-.-.-
- UniProt
- Q92ZP9
- Ligands
- FES, NCO, 3BY, FE, OXY, CYN
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.759 · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | monoxygenase; demethylase (EC 1.-.-.-) | protein | 415 | 33% helix, 24% strand | Q92ZP9 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · chains A
- NCO · Cobalt hexammine(iii) · ligand · chains A
- 3BY · 1-methyl-L-proline · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- OXY · Oxygen molecule · ion · chains A
- CYN · Cyanide ion · ion · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.78 | 0.98 | 28 | 3BY, OXY, CYN |
| 2 | 101 | 0.44 | 0.79 | 30 | empty |
| 3 | 123 | 0.43 | 0.77 | 18 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4QUR · Crystal structure of stachydrine demethylase in complex with cyanide, oxygen, and… · the same entry in another collection · 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 Q92ZP9
- Elsewhere: RCSB PDB 4QUR · PDBe 4QUR · UniProt Q92ZP9
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