Research workbench
Structure of the thioalkalivibrio nitratireducens cytochrome C nitrite reductase in complex with phosphate
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
- 3GM6
- Type
- protein
- Length
- 1,040 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eight-heme nitrite reductase
- UniProt
- Q5F2I3
- Ligands
- HEC, CA, PO4
- Pockets
- 8 · best druggability 0.88
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 | 520 | 45% helix, 10% strand | Q5F2I3 |
Ligands and binding sites
- HEC · Heme C · ligand · 16 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.88 | 0.91 | 97 | HEC, PO4 |
| 2 | 499 | 0.86 | 0.92 | 81 | HEC, PO4 |
| 3 | 368 | 0.83 | 0.91 | 46 | HEC |
| 4 | 198 | 0.78 | 0.92 | 37 | HEC |
| 5 | 367 | 0.57 | 0.75 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 1282 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 cofactor (heme c attachment).
Compared structures
- 3GM6 · Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in… · the same entry in another collection · chain B against B, 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 3GM6 · PDBe 3GM6 · UniProt Q5F2I3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.