Research workbench
Crystal structure of indigo reductase from bacillus smithii type strain dsm 4216
Analyse Crystal structure of indigo reductase from bacillus smithii type strain dsm 4216 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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