MolNFT v1 · #154017 · protein
Crystal structure of indigo reductase from bacillus smithii type strain dsm 4216
6JXN · FMN-dependent NADH-azoreductase: “Crystal structure of indigo reductase from bacillus smithii type strain dsm 4216”. X-ray diffraction, 1 ligand (FMN), 7 pockets (best druggability 0.69). MolNFT v1 #154017 on GenesisL1: 3D…
- PDB
- 6JXN
- Type
- protein
- Length
- 843 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FMN-dependent NADH-azoreductase
- EC
- 1.7.-.-
- UniProt
- G9QLG5
- Ligands
- FMN
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FMN-dependent NADH-azoreductase (EC 1.7.-.-) | protein | 211 | 45% helix, 20% strand | G9QLG5 |
| B, D | FMN-dependent NADH-azoreductase (EC 1.7.-.-) | protein | 212 | 45% helix, 21% strand | G9QLG5 |
| C | FMN-dependent NADH-azoreductase (EC 1.7.-.-) | protein | 208 | 46% helix, 20% strand | G9QLG5 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, D, B, C
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 3 copies · chains B, C, A, D
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.69 | 0.77 | 45 | empty |
| 2 | 485 | 0.64 | 0.76 | 42 | FMN |
| 3 | 500 | 0.63 | 0.75 | 42 | NHE, FMN |
| 4 | 478 | 0.63 | 0.76 | 40 | FMN |
| 5 | 401 | 0.59 | 0.75 | 36 | FMN |
Interfaces
3 interfaces between chains.
- A–D · 1253 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1248 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 717 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6JXN · Crystal Structure of Indigo reductase from Bacillus smithii type strain DSM 4216 · 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 G9QLG5
- Elsewhere: RCSB PDB 6JXN · PDBe 6JXN · UniProt G9QLG5
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