MolNFT v1 · #166769 · protein
Crystal structure of cytochrome C nitrite reductase from the bacterium geobacter lovleyi with bound sulfate
6V0A · Nitrite reductase (cytochrome: “Crystal structure of cytochrome C nitrite reductase from the bacterium geobacter lovleyi with bound sulfate”. X-ray diffraction, 2 ligands (HEC, SO4), 20 pockets (best druggability 0.90). MolNFT v1…
- PDB
- 6V0A
- Type
- protein
- Length
- 2,657 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrite reductase (cytochrome
- EC
- 1.7.2.2
- UniProt
- B3E641
- Ligands
- HEC, SO4
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 6 distinct chains · 51% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrite reductase (cytochrome (EC 1.7.2.2) | protein | 443 | 52% helix, 5% strand | B3E641 |
| B | Nitrite reductase (cytochrome (EC 1.7.2.2) | protein | 444 | 51% helix, 5% strand | B3E641 |
| C | Nitrite reductase (cytochrome (EC 1.7.2.2) | protein | 442 | 52% helix, 5% strand | B3E641 |
| D | Nitrite reductase (cytochrome (EC 1.7.2.2) | protein | 444 | 51% helix, 5% strand | B3E641 |
| E | Nitrite reductase (cytochrome (EC 1.7.2.2) | protein | 443 | 50% helix, 5% strand | B3E641 |
| F | Nitrite reductase (cytochrome (EC 1.7.2.2) | protein | 441 | 50% helix, 5% strand | B3E641 |
Ligands and binding sites
- HEC · Heme C · ligand · 30 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.90 | 0.93 | 128 | HEC, SO4 |
| 2 | 774 | 0.89 | 0.93 | 104 | HEC, SO4 |
| 3 | 755 | 0.89 | 0.93 | 101 | HEC, SO4 |
| 4 | 711 | 0.89 | 0.93 | 99 | HEC, SO4 |
| 5 | 679 | 0.88 | 0.93 | 94 | HEC, SO4 |
Interfaces
6 interfaces between chains.
- A–B · 1726 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1647 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1632 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 450 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 215 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 57 cofactor (heme c attachment).
Compared structures
- 6V0A · Crystal structure of cytochrome c nitrite reductase from the bacterium Geobacter lovleyi… · 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 B3E641
- Elsewhere: RCSB PDB 6V0A · PDBe 6V0A · UniProt B3E641
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.