MolNFT v1 · #90361 · protein
Crystal structure of the flavohem-like-FAD/NAD binding domain of nitric oxide dioxygenase from vibrio cholerae O1 biovar el tor
4EH1 · Flavohemoprotein: “Crystal structure of the flavohem-like-FAD/NAD binding domain of nitric oxide dioxygenase from vibrio…”. X-ray diffraction, 3 ligands (FAD, CL, SO4), 9 pockets (best druggability 0.61). MolNFT v1 #90361 on…
- PDB
- 4EH1
- Type
- protein
- Length
- 474 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavohemoprotein
- EC
- 1.14.12.17
- UniProt
- Q9KMY3
- Ligands
- FAD, CL, SO4
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flavohemoprotein (EC 1.14.12.17) | protein | 237 | 24% helix, 32% strand | Q9KMY3 |
| B | Flavohemoprotein (EC 1.14.12.17) | protein | 237 | 24% helix, 32% strand | Q9KMY3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.61 | 0.78 | 43 | FAD, CL |
| 2 | 88 | 0.54 | 0.85 | 20 | empty |
| 3 | 141 | 0.51 | 0.80 | 25 | CL |
| 4 | 166 | 0.50 | 0.78 | 19 | FAD |
| 5 | 158 | 0.48 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 791 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4EH1 · Crystal Structure of the Flavohem-like-FAD/NAD Binding Domain of Nitric Oxide Dioxygenase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KMY3 · AlphaFold monomer V2.0 prediction for flavohemoprotein (Q9KMY3) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9KMY3
- Elsewhere: RCSB PDB 4EH1 · PDBe 4EH1 · UniProt Q9KMY3
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