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
- 3BM2
- Type
- protein
- Length
- 331 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
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein ydja (EC 1.5.1.34) | protein | 165 | 45% helix, 22% strand | P0ACY1 |
| B | Protein ydja (EC 1.5.1.34) | protein | 166 | 47% helix, 21% strand | P0ACY1 |
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 | 247 | 0.67 | 0.84 | 37 | empty |
| 2 | 254 | 0.60 | 0.80 | 42 | empty |
| 3 | 105 | 0.44 | 0.78 | 19 | empty |
| 4 | 110 | 0.43 | 0.77 | 17 | empty |
| 5 | 63 | 0.35 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2757 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3BM2 · 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 A against A, TM-score 0.90
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 3BM2 · PDBe 3BM2 · UniProt P0ACY1
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