Research workbench
Conformational changes occurring upon reduction in nitrite reductase from pseudomonas aeruginosa
Analyse Conformational changes occurring upon reduction in nitrite reductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BL9
- Type
- protein
- Length
- 1,074 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrite reductase
- EC
- 1.9.3.2
- UniProt
- P24474
- Ligands
- HEC, DHE, OH
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nitrite reductase (EC 1.9.3.2) | protein | 537 | 15% helix, 37% strand | P24474 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B
- DHE · Heme D · ligand · 2 copies · chains A, B
- OH · Hydroxide ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.86 | 0.88 | 106 | HEC, DHE |
| 2 | 555 | 0.84 | 0.90 | 70 | OH, DHE |
| 3 | 470 | 0.84 | 0.91 | 54 | empty |
| 4 | 914 | 0.77 | 0.80 | 69 | empty |
| 5 | 315 | 0.69 | 0.83 | 40 | HEC |
Interfaces
1 interface between chains.
- A–B · 3190 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 1BL9 · Conformational changes occurring upon reduction in nitrite reductase from pseudomonas… · the same entry in another collection · chain A against A, TM-score 1.00
- P24474 · AlphaFold monomer V2.0 prediction for nitrite reductase (P24474) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P24474
- Elsewhere: RCSB PDB 1BL9 · PDBe 1BL9 · UniProt P24474
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