MolNFT v1 · #127907 · protein
Pseudomonas fluorescens kynurenine 3-monooxygenase (kmo) in complex with the enzyme substrate L-kynurenine
5NAK: “Pseudomonas fluorescens kynurenine 3-monooxygenase (kmo) in complex with the enzyme substrate L-kynurenine”. X-ray diffraction, 3 ligands (FAD, KYN, CL), 7 pockets (best druggability 0.83). MolNFT v1 #127907 on GenesisL1: 3D…
- PDB
- 5NAK
- Type
- protein
- Length
- 898 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, KYN, CL
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kynurenine 3-monooxygenase (EC 1.14.13.9) | protein | 451 | 41% helix, 21% strand | Q84HF5 |
| B | Kynurenine 3-monooxygenase (EC 1.14.13.9) | protein | 447 | 41% helix, 21% strand | Q84HF5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- KYN · (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 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 | 1119 | 0.83 | 0.84 | 109 | FAD, CL, GOL |
| 2 | 399 | 0.78 | 0.87 | 33 | empty |
| 3 | 835 | 0.77 | 0.80 | 83 | FAD, CL, GOL, KYN |
| 4 | 216 | 0.74 | 0.89 | 29 | empty |
| 5 | 75 | 0.36 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 637 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5NAK · Pseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in complex with the enzyme… · the same entry in another collection · chain B against B, 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 5NAK · PDBe 5NAK · UniProt Q84HF5
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