MolNFT v1 · #79252 · protein
Structure of a hexameric multiheme C nitrite reductase from the extremophile bacterium thiolkalivibrio paradoxus
3SXQ · Eight-heme nitrite reductase: “Structure of a hexameric multiheme C nitrite reductase from the extremophile bacterium thiolkalivibrio…”. X-ray diffraction, 6 ligands (HEC, CO, CA), 4 pockets (best druggability 0.90). MolNFT v1…
- PDB
- 3SXQ
- Type
- protein
- Length
- 1,036 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eight-heme nitrite reductase
- UniProt
- E7EDQ7
- Ligands
- HEC, CO, CA, NA, SO4, CL
- Pockets
- 4 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eight-heme nitrite reductase | protein | 519 | 44% helix, 10% strand | E7EDQ7 |
| B | Eight-heme nitrite reductase | protein | 517 | 45% helix, 10% strand | E7EDQ7 |
Ligands and binding sites
- HEC · Heme C · ligand · 16 copies · chains A, B
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.90 | 0.91 | 135 | HEC, CO |
| 2 | 1142 | 0.89 | 0.90 | 141 | HEC, CO |
| 3 | 365 | 0.55 | 0.74 | 38 | empty |
| 4 | 213 | 0.54 | 0.78 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1139 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 cofactor (heme c attachment).
Compared structures
- 3SXQ · Structure of a hexameric multiheme c nitrite reductase from the extremophile bacterium… · 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 E7EDQ7
- Elsewhere: RCSB PDB 3SXQ · PDBe 3SXQ · UniProt E7EDQ7
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