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Crystal structure of as isolated Y323E mutant of haem-cu containing nitrite reductase from ralstonia pickettii
Analyse Crystal structure of as isolated Y323E 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
- 6QPZ
- Type
- protein
- Length
- 911 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
- I6NAW4
- Ligands
- HEC, CU
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 455 | 22% helix, 34% strand | I6NAW4 |
| I | Copper-containing nitrite reductase (EC 1.7.2.1) | protein | 456 | 21% helix, 34% strand | I6NAW4 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, I
- CU · Copper (II) ion · metal · 4 copies · chains A, I
- GOL · Glycerol · additive · chains I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.77 | 0.85 | 59 | HEC |
| 2 | 553 | 0.75 | 0.82 | 68 | HEC |
| 3 | 163 | 0.44 | 0.75 | 31 | empty |
| 4 | 151 | 0.44 | 0.75 | 30 | empty |
| 5 | 64 | 0.43 | 0.82 | 17 | 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
- 6QPZ · Crystal structure of as isolated Y323E 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 I6NAW4
- Elsewhere: RCSB PDB 6QPZ · PDBe 6QPZ · UniProt I6NAW4
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