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Structure of the thioalkalivibrio nitratireducens cytochrome C nitrite reductase in complex with cyanide
Analyse Structure of the thioalkalivibrio nitratireducens cytochrome C nitrite… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MMO
- 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
- Q5F2I3
- Ligands
- HEC, NA, CA, CYN
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Eight-heme nitrite reductase | protein | 518 | 43% helix, 10% strand | Q5F2I3 |
Ligands and binding sites
- HEC · Heme C · ligand · 16 copies · chains A, B
- NA · Sodium ion · metal · 6 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- CYN · Cyanide ion · ion · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 15 copies · chains A, B
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 3 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.88 | 0.89 | 103 | HEC, CYN, CA |
| 2 | 393 | 0.84 | 0.93 | 69 | HEC, CYN |
| 3 | 375 | 0.82 | 0.91 | 43 | HEC |
| 4 | 207 | 0.78 | 0.92 | 38 | HEC |
| 5 | 124 | 0.74 | 0.93 | 32 | HEC |
Interfaces
1 interface between chains.
- A–B · 1295 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 cofactor (heme c attachment).
Compared structures
- 3MMO · Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in… · 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 Q5F2I3
- Elsewhere: RCSB PDB 3MMO · PDBe 3MMO · UniProt Q5F2I3
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