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The crystal structure of flavohemoglobin from R. eutrophus in complex with econazole
Analyse The crystal structure of flavohemoglobin from R. eutrophus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OZV
- Type
- protein
- Length
- 806 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavohemoglobin
- EC
- 1.14.12.17
- UniProt
- P39662
- Ligands
- HEM, FAD, DGG, ECN, PO4
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Flavohemoglobin (EC 1.14.12.17) | protein | 403 | 42% helix, 19% strand | P39662 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, A
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains B, A
- DGG · 1-[glycerolylphosphonyl]-2-[8-(2-hexyl-cyclopropyl)-octanal-1-yl]-3-[hexadecanal-1-yl]-glycerol · ligand · 2 copies · chains B, A
- ECN · 1-[(2S)-2-[(4-chlorobenzyl)oxy]-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole · ligand · 2 copies · chains B, A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.87 | 0.88 | 83 | HEM, FAD, DGG, ECN |
| 2 | 818 | 0.87 | 0.89 | 81 | HEM, FAD, DGG, ECN |
| 3 | 221 | 0.76 | 0.90 | 33 | empty |
| 4 | 118 | 0.39 | 0.75 | 20 | empty |
| 5 | 82 | 0.38 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 1278 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3OZV · The Crystal Structure of flavohemoglobin from R. eutrophus in complex with econazole · the same entry in another collection · chain B against B, TM-score 1.00
- P39662 · AlphaFold monomer V2.0 prediction for flavohemoprotein (P39662) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P39662
- Elsewhere: RCSB PDB 3OZV · PDBe 3OZV · UniProt P39662
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