Research workbench
Crystal structure of the nitroreductase family protein from streptococcus pneumoniae TIGR4
Analyse Crystal structure of the nitroreductase family protein from streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B67
- Type
- protein
- Length
- 802 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- COG0778: nitroreductase
- EC
- 1.6.99.3
- UniProt
- Q97S03
- Ligands
- FMN
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | COG0778: nitroreductase (EC 1.6.99.3) | protein | 201 | 50% helix, 18% strand | Q97S03 |
| B, C | COG0778: nitroreductase (EC 1.6.99.3) | protein | 200 | 52% helix, 19% strand | Q97S03 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- ACY · Acetic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.75 | 0.78 | 94 | FMN |
| 2 | 778 | 0.73 | 0.78 | 69 | FMN |
| 3 | 524 | 0.67 | 0.78 | 57 | FMN |
| 4 | 474 | 0.65 | 0.77 | 53 | FMN |
| 5 | 61 | 0.38 | 0.79 | 12 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3306 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 3221 Ų buried · 65 hydrogen bonds · protein-protein
- A–C · 374 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 138 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 2B67 · Crystal structure of the Nitroreductase Family Protein from Streptococcus pneumoniae TIGR4 · 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 Q97S03
- Elsewhere: RCSB PDB 2B67 · PDBe 2B67 · UniProt Q97S03
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