MolNFT v1 · #81553 · protein
Structure of the free tvnirb form of thioalkalivibrio nitratireducens cytochrome C nitrite reductase
3UU9 · Eight-heme nitrite reductase: “Structure of the free tvnirb form of thioalkalivibrio nitratireducens cytochrome C nitrite reductase”. X-ray diffraction, 3 ligands (HEC, CA, NA), 5 pockets (best druggability 0.89). MolNFT v1 #81553…
- PDB
- 3UU9
- Type
- protein
- Length
- 1,039 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eight-heme nitrite reductase
- EC
- 1.7.2.-
- UniProt
- Q5F2I3
- Ligands
- HEC, CA, NA
- Pockets
- 5 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eight-heme nitrite reductase (EC 1.7.2.-) | protein | 519 | 45% helix, 10% strand | Q5F2I3 |
| B | Eight-heme nitrite reductase (EC 1.7.2.-) | protein | 520 | 45% helix, 10% strand | Q5F2I3 |
Ligands and binding sites
- HEC · Heme C · ligand · 16 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · chains B
- PG4 · Tetraethylene glycol · additive · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.89 | 0.91 | 147 | HEC |
| 2 | 811 | 0.88 | 0.91 | 107 | HEC, CA, NA |
| 3 | 359 | 0.82 | 0.91 | 47 | HEC |
| 4 | 250 | 0.58 | 0.79 | 28 | empty |
| 5 | 299 | 0.53 | 0.75 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 1307 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 cofactor, 2 covalent (heme c attachment, additive adduct).
Compared structures
- 3UU9 · Structure of the free TvNiRb form of Thioalkalivibrio nitratireducens cytochrome c… · 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 3UU9 · PDBe 3UU9 · UniProt Q5F2I3
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