MolNFT v1 · #9035 · protein
Cytochrome CD1 nitrite reductase, reoxidised enzyme
1HJ5: “Cytochrome CD1 nitrite reductase, reoxidised enzyme”. X-ray diffraction, 3 ligands (HEC, DHE, SO4), 7 pockets (best druggability 0.86). MolNFT v1 #9035 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1HJ5
- Type
- protein
- Length
- 1,118 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrite reductase
- EC
- 1.7.2.1, 1.7.99.1
- UniProt
- P72181
- Ligands
- HEC, DHE, SO4
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nitrite reductase (EC 1.7.2.1, 1.7.99.1) | protein | 559 | 17% helix, 36% strand | P72181 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B
- DHE · Heme D · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · 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 | 351 | 0.86 | 0.95 | 47 | DHE |
| 2 | 677 | 0.85 | 0.88 | 87 | HEC, DHE, GOL |
| 3 | 227 | 0.84 | 0.96 | 32 | empty |
| 4 | 1128 | 0.76 | 0.78 | 93 | empty |
| 5 | 336 | 0.71 | 0.84 | 53 | HEC, GOL |
Interfaces
1 interface between chains.
- A–B · 1376 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
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 P72181
- Elsewhere: RCSB PDB 1HJ5 · PDBe 1HJ5 · UniProt P72181
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