MolNFT v1 · #82370 · protein
Assimilatory nitrite reductase (NII3) - NO2 complex from tobbaco leaf analysed with middle X-ray dose
3VKQ: “Assimilatory nitrite reductase (NII3) - NO2 complex from tobbaco leaf analysed with middle X-ray dose”. X-ray diffraction, 5 ligands (SRM, SF4, K), 4 pockets (best druggability 0.78). MolNFT v1 #82370 on GenesisL1: 3D structure…
- PDB
- 3VKQ
- Type
- protein
- Length
- 538 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrite reductase
- EC
- 1.7.7.1
- UniProt
- Q76KB0
- Ligands
- SRM, SF4, K, CL, NO2
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrite reductase (EC 1.7.7.1) | protein | 538 | 37% helix, 23% strand | Q76KB0 |
Ligands and binding sites
- SRM · Siroheme · ligand · chains A
- SF4 · Iron/sulfur cluster · ligand · chains A
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- NO2 · Nitrite ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.78 | 0.84 | 61 | SRM, SF4, CL, NO2 |
| 2 | 207 | 0.56 | 0.79 | 29 | empty |
| 3 | 130 | 0.44 | 0.76 | 22 | empty |
| 4 | 87 | 0.36 | 0.76 | 17 | empty |
Compared structures
- 3VKQ · Assimilatory nitrite reductase (Nii3) - NO2 complex from tobbaco leaf analysed with… · 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 Q76KB0
- Elsewhere: RCSB PDB 3VKQ · PDBe 3VKQ · UniProt Q76KB0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.