MolNFT v1 · #161814 · protein
Crystal structure of nitrite bound Y323A mutant of haem-cu containing nitrite reductase from ralstonia pickettii
6QPX · Copper-containing nitrite reductase: “Crystal structure of nitrite bound Y323A mutant of haem-cu containing nitrite reductase from ralstonia…”. X-ray diffraction, 3 ligands (HEC, CU, NO2), 13 pockets (best druggability 0.76). MolNFT…
- PDB
- 6QPX
- Type
- protein
- Length
- 909 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper-containing nitrite reductase
- EC
- 1.7.2.1
- UniProt
- U3G913
- Ligands
- HEC, CU, NO2
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 454 | 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
- HEC · Heme C · ligand · 2 copies · chains A, I
- CU · Copper (II) ion · metal · 4 copies · chains A, I
- NO2 · Nitrite ion · ion · 2 copies · chains A, I
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 | 504 | 0.76 | 0.84 | 61 | HEC |
| 2 | 232 | 0.76 | 0.89 | 36 | HEC |
| 3 | 321 | 0.59 | 0.77 | 40 | empty |
| 4 | 182 | 0.48 | 0.76 | 32 | empty |
| 5 | 140 | 0.43 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–I · 92 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 6QPX · Crystal structure of nitrite bound 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 6QPX · PDBe 6QPX · UniProt U3G913
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