MolNFT v1 · #4926 · protein
Cytochrome CD1 nitrite reductase, reduced and cyanide bound
1E2R: “Cytochrome CD1 nitrite reductase, reduced and cyanide bound”. X-ray diffraction, 3 ligands (HEC, DHE, CYN), 7 pockets (best druggability 0.84). MolNFT v1 #4926 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1E2R
- Type
- protein
- Length
- 1,075 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, CYN
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrite reductase (EC 1.7.2.1, 1.7.99.1) | protein | 532 | 17% helix, 38% strand | P72181 |
| B | Nitrite reductase (EC 1.7.2.1, 1.7.99.1) | protein | 543 | 17% helix, 37% strand | P72181 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B
- DHE · Heme D · ligand · 2 copies · chains A, B
- CYN · Cyanide ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.84 | 0.97 | 33 | empty |
| 2 | 535 | 0.80 | 0.87 | 58 | DHE, CYN, GOL |
| 3 | 925 | 0.75 | 0.78 | 67 | empty |
| 4 | 646 | 0.75 | 0.81 | 75 | DHE, CYN |
| 5 | 171 | 0.63 | 0.83 | 27 | HEC |
Interfaces
1 interface between chains.
- A–B · 1559 Ų buried · 29 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 1E2R · PDBe 1E2R · UniProt P72181
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