Research workbench
Structural studies on a prodrug-activating system-CB1954 and FMN- dependent nitroreductase
Analyse Structural studies on a prodrug-activating system-CB1954 and FMN- dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IDT
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Minor FMN-dependent nitroreductase
- EC
- 1.6.99.7
- UniProt
- P38489
- Ligands
- FMN, CB1
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Minor FMN-dependent nitroreductase (EC 1.6.99.7) | protein | 217 | 55% helix, 15% strand | P38489 |
| B | Minor FMN-dependent nitroreductase (EC 1.6.99.7) | protein | 216 | 53% helix, 15% strand | P38489 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- CB1 · 5-(aziridin-1-yl)-2,4-dinitrobenzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.75 | 0.84 | 44 | FMN, CB1 |
| 2 | 512 | 0.72 | 0.81 | 43 | CB1, FMN |
| 3 | 206 | 0.52 | 0.77 | 23 | empty |
| 4 | 182 | 0.51 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 3605 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 1IDT · Structural studies on a prodrug-activating system-CB1954 and FMN-dependent nitroreductase · the same entry in another collection · chain A against A, TM-score 1.00
- P38489 · AlphaFold monomer V2.0 prediction for oxygen-insensitive NAD(P)H nitroreductase (P38489) · a predicted model of the same protein · chain B 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 P38489
- Elsewhere: RCSB PDB 1IDT · PDBe 1IDT · UniProt P38489
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