MolNFT v1 · #125884 · protein
Oxidized flavodiiron core of escherichia COLI flavorubredoxin, including the fe-4SG atoms from its rubredoxin domain
5LMC · Anaerobic nitric oxide reductase flavorubredoxin: “Oxidized flavodiiron core of escherichia COLI flavorubredoxin, including the fe-4SG atoms from its rubredoxin…”. X-ray diffraction, 4 ligands (FEO, FMN, FE), 5 pockets (best…
- PDB
- 5LMC
- Type
- protein
- Length
- 399 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anaerobic nitric oxide reductase flavorubredoxin
- UniProt
- Q46877
- Ligands
- FEO, FMN, FE, PO4
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anaerobic nitric oxide reductase flavorubredoxin | protein | 399 | 37% helix, 25% strand | Q46877 |
Ligands and binding sites
- FEO · Mu-oxo-diiron · ligand · chains A
- FMN · Flavin mononucleotide · ligand · chains A
- FE · Fe (III) ion · metal
- PO4 · Phosphate ion · ion · 2 copies · chains A
- CAC · Cacodylate ion · additive · chains A
- ACY · Acetic acid · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.53 | 0.86 | 17 | empty |
| 2 | 57 | 0.39 | 0.80 | 20 | PO4 |
| 3 | 57 | 0.36 | 0.79 | 18 | FMN |
| 4 | 67 | 0.33 | 0.76 | 11 | empty |
| 5 | 65 | 0.30 | 0.74 | 15 | empty |
Compared structures
- 5LMC · Oxidized flavodiiron core of Escherichia coli flavorubredoxin, including the Fe-4SG atoms… · the same entry in another collection · chain A against A, TM-score 1.00
- Q46877 · AlphaFold monomer V2.0 prediction for anaerobic nitric oxide reductase flavorubredoxin… · a predicted model of the same protein · 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 Q46877
- Elsewhere: RCSB PDB 5LMC · PDBe 5LMC · UniProt Q46877
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