MolNFT v1 · #7869 · protein
Pseudomonas aeruginosa CD1 nitrite reductase reduced cyanide complex
1GJQ: “Pseudomonas aeruginosa CD1 nitrite reductase reduced cyanide complex”. X-ray diffraction, 3 ligands (HEC, DHE, CYN), 8 pockets (best druggability 0.84). MolNFT v1 #7869 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1GJQ
- Type
- protein
- Length
- 1,080 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, CYN
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrite reductase (EC 1.9.3.2) | protein | 541 | 16% helix, 38% strand | P24474 |
| B | Nitrite reductase (EC 1.9.3.2) | protein | 539 | 16% helix, 38% strand | P24474 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.84 | 0.90 | 72 | DHE, CYN |
| 2 | 664 | 0.84 | 0.88 | 84 | DHE, CYN |
| 3 | 472 | 0.84 | 0.91 | 56 | empty |
| 4 | 902 | 0.78 | 0.80 | 72 | empty |
| 5 | 335 | 0.70 | 0.83 | 46 | HEC |
Interfaces
1 interface between chains.
- A–B · 3488 Ų buried · 40 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 P24474
- Elsewhere: RCSB PDB 1GJQ · PDBe 1GJQ · UniProt P24474
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