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Crystal structure of as isolated Y323A mutant of haem-Cu containing nitrite reductase from Ralstonia pickettii
Analyse Crystal structure of as isolated Y323A mutant of haem-Cu containing nitrite… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QPV
- Type
- protein
- Length
- 910 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Ralstonia pickettii
- Molecule
- Copper-containing nitrite reductase
- EC
- 1.7.2.1
- UniProt
- U3G913
- Ligands
- HEC, CU
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.6 · 2 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 455 | 21% helix, 34% strand | U3G913 |
| I | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 455 | 22% helix, 33% strand | U3G913 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.76 | 0.84 | 67 | HEC |
| 2 | 227 | 0.75 | 0.89 | 36 | HEC |
| 3 | 308 | 0.58 | 0.77 | 38 | empty |
| 4 | 64 | 0.46 | 0.83 | 20 | empty |
| 5 | 63 | 0.44 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–I · 93 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 6QPV · Crystal structure of as isolated Y323A mutant of haem-cu containing nitrite reductase… · 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 U3G913
- Elsewhere: RCSB PDB 6QPV · PDBe 6QPV · UniProt U3G913
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