MolNFT v1 · #28378 · protein
X-ray structures of moorella thermoacetica fpra. novel diiron site structure and mechanistic insights into a scavenging nitric oxide reductase
1YCG: “X-ray structures of moorella thermoacetica fpra. novel diiron site structure and mechanistic insights into a…”. X-ray diffraction, 3 ligands (FEO, FMN, ZN), 10 pockets (best druggability 0.78). MolNFT v1 #28378 on GenesisL1: 3D…
- PDB
- 1YCG
- Type
- protein
- Length
- 1,592 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide reductase
- EC
- 1.-.-.-
- UniProt
- Q9FDN7
- Ligands
- FEO, FMN, ZN
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Nitric oxide reductase (EC 1.-.-.-) | protein | 398 | 38% helix, 23% strand | Q9FDN7 |
Ligands and binding sites
- FEO · Mu-oxo-diiron · ligand · 4 copies · chains A, B, C, D
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 14 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.78 | 0.82 | 83 | FMN |
| 2 | 338 | 0.76 | 0.87 | 51 | FMN |
| 3 | 321 | 0.75 | 0.86 | 48 | FMN |
| 4 | 347 | 0.75 | 0.86 | 57 | FMN |
| 5 | 404 | 0.66 | 0.79 | 34 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1790 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1712 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 379 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (additive adduct).
Compared structures
- 1YCG · X-ray Structures of Moorella thermoacetica FprA. Novel Diiron Site Structure and… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9FDN7 · AlphaFold monomer V2.0 prediction for nitric oxide reductase (Q9FDN7) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9FDN7
- Elsewhere: RCSB PDB 1YCG · PDBe 1YCG · UniProt Q9FDN7
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