Research workbench
Crystal structure of coenzyme F420H2 oxidase (fpra), a diiron flavoprotein, active 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
- 2OHH
- 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, SO4
- Pockets
- 18 · best druggability 0.81
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 · 8 copies · chains A, B, D, E
- SO4 · Sulfate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.81 | 0.82 | 72 | empty |
| 2 | 1107 | 0.81 | 0.82 | 75 | empty |
| 3 | 253 | 0.75 | 0.88 | 37 | FMN |
| 4 | 858 | 0.75 | 0.79 | 81 | empty |
| 5 | 109 | 0.73 | 0.93 | 29 | empty |
Interfaces
4 interfaces between chains.
- D–E · 2065 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2033 Ų buried · 28 hydrogen bonds · protein-protein
- B–E · 1488 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1486 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2OHH · Crystal Structure of coenzyme F420H2 oxidase (FprA), a diiron flavoprotein, active… · 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 A 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 2OHH · PDBe 2OHH · UniProt Q50497
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