MolNFT v1 · #127903 · protein
Pseudomonas fluorescens kynurenine 3-monooxygenase (kmo) in complex with 3-{5-chloro-6-[(1R)-1-(pyridin-2-YL)ETHOXY]-1,2-benzoxazol-3- YL}PROPANOIC acid
5NAG: “Pseudomonas fluorescens kynurenine 3-monooxygenase (kmo) in complex with…”. X-ray diffraction, 2 ligands (FAD, 8R5), 7 pockets (best druggability 0.81). MolNFT v1 #127903 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NAG
- Type
- protein
- Length
- 899 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kynurenine 3-monooxygenase
- EC
- 1.14.13.9
- UniProt
- Q84HF5
- Ligands
- FAD, 8R5
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kynurenine 3-monooxygenase (EC 1.14.13.9) | protein | 448 | 41% helix, 22% strand | Q84HF5 |
| B | Kynurenine 3-monooxygenase (EC 1.14.13.9) | protein | 451 | 43% helix, 22% strand | Q84HF5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 8R5 · 3-[5-chloranyl-6-[(1~{R})-1-pyridin-2-ylethoxy]-1,2-benzoxazol-3-yl]propanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.81 | 0.82 | 83 | empty |
| 2 | 890 | 0.78 | 0.81 | 76 | FAD, 8R5 |
| 3 | 840 | 0.77 | 0.81 | 77 | FAD, 8R5 |
| 4 | 578 | 0.70 | 0.79 | 40 | empty |
| 5 | 67 | 0.38 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 440 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5NAG · Pseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q84HF5 · AlphaFold monomer V2.0 prediction for kynurenine 3-monooxygenase (Q84HF5) · 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 Q84HF5
- Elsewhere: RCSB PDB 5NAG · PDBe 5NAG · UniProt Q84HF5
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