MolNFT v1 · #191392 · protein
Crystal structure of putative nitroreductase from salmonella enterica
8DIL · Putative NAD(P)H nitroreductase: “Crystal structure of putative nitroreductase from salmonella enterica”. X-ray diffraction, 1 ligand (FMN), 12 pockets (best druggability 0.67). MolNFT v1 #191392 on GenesisL1: 3D structure, binding…
- PDB
- 8DIL
- Type
- protein
- Length
- 1,043 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative NAD(P)H nitroreductase
- EC
- 1.-.-.-
- UniProt
- A0A0H3NAL3
- Ligands
- FMN
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative NAD(P)H nitroreductase (EC 1.-.-.-) | protein | 175 | 47% helix, 20% strand | A0A0H3NAL3 |
| B, D, E, F | Putative NAD(P)H nitroreductase (EC 1.-.-.-) | protein | 174 | 48% helix, 20% strand | A0A0H3NAL3 |
| C | Putative NAD(P)H nitroreductase (EC 1.-.-.-) | protein | 172 | 47% helix, 21% strand | A0A0H3NAL3 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D, E
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains A, C, D, B, E, F
- CIT · Citric acid · additive · 6 copies · chains A, B, C, D, E, F
- PGE · Triethylene glycol · additive · 5 copies · chains A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.67 | 0.78 | 77 | FMN, CIT |
| 2 | 373 | 0.63 | 0.78 | 48 | FMN, CIT |
| 3 | 286 | 0.60 | 0.78 | 40 | FMN, CIT |
| 4 | 199 | 0.59 | 0.81 | 36 | FMN, CIT |
| 5 | 272 | 0.58 | 0.78 | 39 | FMN, CIT |
Interfaces
5 interfaces between chains.
- C–D · 2925 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2891 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 2888 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 632 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 586 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 8DIL · Crystal structure of putative nitroreductase from Salmonella enterica · 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 A0A0H3NAL3
- Elsewhere: RCSB PDB 8DIL · PDBe 8DIL · UniProt A0A0H3NAL3
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