MolNFT v1 · #146944 · protein
The crystal structure of an FMN-dependent NADH-azoreductase from klebsiella pneumoniae
6DXP: “The crystal structure of an FMN-dependent NADH-azoreductase from klebsiella pneumoniae”. X-ray diffraction, 1 ligand (FMN), 7 pockets (best druggability 0.87). MolNFT v1 #146944 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6DXP
- Type
- protein
- Length
- 815 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FMN-dependent NADH-azoreductase
- EC
- 1.7.-.-
- UniProt
- A0A1W1JPX6
- Ligands
- FMN
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FMN-dependent NADH-azoreductase (EC 1.7.-.-) | protein | 206 | 45% helix, 20% strand | A0A1W1JPX6 |
| C | FMN-dependent NADH-azoreductase (EC 1.7.-.-) | protein | 200 | 42% helix, 19% strand | A0A1W1JPX6 |
| B | FMN-dependent NADH-azoreductase (EC 1.7.-.-) | protein | 204 | 43% helix, 19% strand | A0A1W1JPX6 |
| D | FMN-dependent NADH-azoreductase (EC 1.7.-.-) | protein | 205 | 41% helix, 21% strand | A0A1W1JPX6 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.87 | 0.89 | 138 | empty |
| 2 | 613 | 0.78 | 0.84 | 69 | empty |
| 3 | 293 | 0.68 | 0.83 | 36 | FMN |
| 4 | 308 | 0.67 | 0.82 | 33 | FMN |
| 5 | 245 | 0.67 | 0.83 | 32 | FMN |
Interfaces
6 interfaces between chains.
- A–B · 1815 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1767 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 727 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 429 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 344 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6DXP · The crystal structure of an FMN-dependent NADH-azoreductase from Klebsiella pneumoniae · 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 A0A1W1JPX6
- Elsewhere: RCSB PDB 6DXP · PDBe 6DXP · UniProt A0A1W1JPX6
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