Research workbench
Crystal structure of coenzyme F420H2 oxidase (fpra), a diiron flavoprotein, inactive oxidized state
Analyse Crystal structure of coenzyme F420H2 oxidase (fpra), a diiron flavoprotein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OHJ
- Type
- protein
- Length
- 1,612 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type a flavoprotein fpra
- EC
- 1.-.-.-
- UniProt
- Q50497
- Ligands
- FMN, FE, CL
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Type a flavoprotein fpra (EC 1.-.-.-) | protein | 403 | 39% helix, 24% strand | Q50497 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, D, E
- FE · Fe (III) ion · metal · 12 copies · chains A, B, D, E
- CL · Chloride ion · ion · 7 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.84 | 0.91 | 49 | FMN |
| 2 | 412 | 0.83 | 0.91 | 46 | FMN |
| 3 | 471 | 0.82 | 0.89 | 53 | FMN |
| 4 | 372 | 0.82 | 0.91 | 42 | FMN |
| 5 | 1157 | 0.81 | 0.82 | 71 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2157 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 2074 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 1485 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 1457 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2OHJ · Crystal Structure of coenzyme F420H2 oxidase (FprA), a diiron flavoprotein, inactive… · the same entry in another collection · chain E against E, TM-score 1.00
- Q50497 · AlphaFold monomer V2.0 prediction for type a flavoprotein fpra (Q50497) · a predicted model of the same protein · chain E 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 Q50497
- Elsewhere: RCSB PDB 2OHJ · PDBe 2OHJ · UniProt Q50497
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