MolNFT v1 · #126095 · protein
Crystal structure of nitronate monooxygenase (SO_0471) from shewanella oneidensis mr-1
5LSM · FMN-dependent nitronate monooxygenase: “Crystal structure of nitronate monooxygenase (SO_0471) from shewanella oneidensis mr-1”. X-ray diffraction, 1 ligand (FMN), 20 pockets (best druggability 0.79). MolNFT v1 #126095 on GenesisL1…
- PDB
- 5LSM
- Type
- protein
- Length
- 2,680 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FMN-dependent nitronate monooxygenase
- EC
- 1.13.12.16
- UniProt
- Q8EJJ2
- Ligands
- FMN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FMN-dependent nitronate monooxygenase (EC 1.13.12.16) | protein | 339 | 40% helix, 14% strand | Q8EJJ2 |
| B | FMN-dependent nitronate monooxygenase (EC 1.13.12.16) | protein | 332 | 39% helix, 15% strand | Q8EJJ2 |
| C | FMN-dependent nitronate monooxygenase (EC 1.13.12.16) | protein | 338 | 39% helix, 14% strand | Q8EJJ2 |
| D | FMN-dependent nitronate monooxygenase (EC 1.13.12.16) | protein | 333 | 41% helix, 14% strand | Q8EJJ2 |
| E | FMN-dependent nitronate monooxygenase (EC 1.13.12.16) | protein | 339 | 39% helix, 14% strand | Q8EJJ2 |
| F | FMN-dependent nitronate monooxygenase (EC 1.13.12.16) | protein | 337 | 40% helix, 15% strand | Q8EJJ2 |
| G | FMN-dependent nitronate monooxygenase (EC 1.13.12.16) | protein | 331 | 39% helix, 15% strand | Q8EJJ2 |
| H | FMN-dependent nitronate monooxygenase (EC 1.13.12.16) | protein | 331 | 40% helix, 15% strand | Q8EJJ2 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 4 copies · chains A, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.79 | 0.89 | 51 | FMN |
| 2 | 405 | 0.79 | 0.88 | 58 | FMN, GOL |
| 3 | 368 | 0.79 | 0.89 | 58 | FMN, GOL |
| 4 | 383 | 0.79 | 0.88 | 56 | FMN |
| 5 | 432 | 0.78 | 0.87 | 57 | FMN |
Interfaces
9 interfaces between chains.
- D–F · 1254 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1221 Ų buried · 14 hydrogen bonds · protein-protein
- E–H · 397 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 381 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 316 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5LSM · Crystal structure of nitronate monooxygenase (SO_0471) from Shewanella oneidensis MR-1 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8EJJ2
- Elsewhere: RCSB PDB 5LSM · PDBe 5LSM · UniProt Q8EJJ2
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