Research workbench
Crystal structure of a minimal nitroreductase ydja from escherichia COLI K12 with and without FMN cofactor
Analyse Crystal structure of a minimal nitroreductase ydja from escherichia COLI K12… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BM1
- Type
- protein
- Length
- 354 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein ydja
- EC
- 1.5.1.34
- UniProt
- P0ACY1
- Ligands
- FMN
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein ydja (EC 1.5.1.34) | protein | 177 | 46% helix, 20% strand | P0ACY1 |
| B | Protein ydja (EC 1.5.1.34) | protein | 177 | 46% helix, 20% strand | P0ACY1 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.60 | 0.78 | 41 | FMN |
| 2 | 255 | 0.60 | 0.79 | 39 | FMN |
Interfaces
1 interface between chains.
- A–B · 2799 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3BM1 · Crystal structure of a minimal nitroreductase ydjA from Escherichia coli K12 with and… · the same entry in another collection · chain A against A, TM-score 1.00
- P0ACY1 · AlphaFold monomer V2.0 prediction for putative NAD(P)H nitroreductase ydja (P0ACY1) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P0ACY1
- Elsewhere: RCSB PDB 3BM1 · PDBe 3BM1 · UniProt P0ACY1
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