Research workbench
Structure of the thioalkalivibrio paradoxus cytochrome C nitrite reductase in complex with sulfite
Analyse Structure of the thioalkalivibrio paradoxus cytochrome C nitrite reductase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TTB
- Type
- protein
- Length
- 1,038 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, SO4, SO3
- Pockets
- 4 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Eight-heme nitrite reductase | protein | 519 | 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
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- SO3 · Sulfite ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 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 | 1107 | 0.90 | 0.91 | 130 | HEC, SO3, CO |
| 2 | 1096 | 0.89 | 0.91 | 133 | HEC, SO3, CO |
| 3 | 374 | 0.56 | 0.74 | 39 | empty |
| 4 | 187 | 0.51 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1197 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 cofactor (heme c attachment).
Compared structures
- 3TTB · Structure of the Thioalkalivibrio paradoxus cytochrome c nitrite reductase in complex… · 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 3TTB · PDBe 3TTB · UniProt E7EDQ7
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