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Crystal structure of putative nitroreductase ydfn (2632848) from bacillus subtilis at 1.65 a resolution
Analyse Crystal structure of putative nitroreductase ydfn (2632848) from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BEM
- Type
- protein
- Length
- 417 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative NAD(P)H nitroreductase ydfn
- EC
- 1.-.-.-
- UniProt
- P96692
- Ligands
- FMN, NI
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative NAD(P)H nitroreductase ydfn (EC 1.-.-.-) | protein | 207 | 52% helix, 15% strand | P96692 |
| B | Putative NAD(P)H nitroreductase ydfn (EC 1.-.-.-) | protein | 210 | 53% helix, 16% strand | P96692 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · chains A, B
- PGO · S-1,2-propanediol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.69 | 0.79 | 42 | ACT, FMN |
| 2 | 484 | 0.65 | 0.77 | 41 | FMN |
| 3 | 90 | 0.37 | 0.76 | 18 | empty |
| 4 | 85 | 0.36 | 0.76 | 19 | empty |
| 5 | 56 | 0.33 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3647 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3BEM · Crystal structure of putative nitroreductase ydfN (2632848) from Bacillus subtilis at… · the same entry in another collection · chain A against A, TM-score 1.00
- P96692 · AlphaFold monomer V2.0 prediction for putative NAD(P)H nitroreductase mhqn (P96692) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P96692
- Elsewhere: RCSB PDB 3BEM · PDBe 3BEM · UniProt P96692
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