MolNFT v1 · #129144 · protein
Crystal structure of nitrite bound D97N mutant of three-domain heme-cu nitrite reductase from ralstonia pickettii
5OBO · Nitrite reductase, copper-containing: “Crystal structure of nitrite bound D97N mutant of three-domain heme-cu nitrite reductase from ralstonia…”. X-ray diffraction, 3 ligands (HEC, CU, NO2), 5 pockets (best druggability 0.76).…
- PDB
- 5OBO
- Type
- protein
- Length
- 456 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrite reductase, copper-containing
- UniProt
- U3G913
- Ligands
- HEC, CU, NO2
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrite reductase, copper-containing | protein | 456 | 21% helix, 33% strand | U3G913 |
Ligands and binding sites
- HEC · Heme C · ligand · chains A
- CU · Copper (II) ion · metal · 2 copies · chains A
- NO2 · Nitrite ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.76 | 0.83 | 67 | HEC |
| 2 | 127 | 0.42 | 0.76 | 30 | empty |
| 3 | 55 | 0.38 | 0.80 | 16 | empty |
| 4 | 104 | 0.37 | 0.75 | 19 | empty |
| 5 | 60 | 0.31 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 2 cofactor (heme c attachment).
Compared structures
- 5OBO · Crystal structure of nitrite bound D97N mutant of three-domain heme-Cu 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 5OBO · PDBe 5OBO · UniProt U3G913
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