MolNFT v1 · #71152 · protein
Crystal structure of putative NADH DEHYDROGENASE/NAD(P)H nitroreductase (BDI_1728) from parabacteroides distasonis atcc 8503 at 1.86 a resolution
3M5K: “Crystal structure of putative NADH DEHYDROGENASE/NAD(P)H nitroreductase (BDI_1728) from parabacteroides…”. X-ray diffraction, 3 ligands (FMN, UNL, CL), 2 pockets (best druggability 0.62). MolNFT v1 #71152 on GenesisL1: 3D structure…
- PDB
- 3M5K
- Type
- protein
- Length
- 336 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative NADH DEHYDROGENASE/NAD(P)H nitroreductase
- UniProt
- A6LCR1
- Ligands
- FMN, UNL, CL
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative NADH DEHYDROGENASE/NAD(P)H nitroreductase | protein | 168 | 42% helix, 20% strand | A6LCR1 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains 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 | 205 | 0.62 | 0.82 | 31 | UNL, FMN |
| 2 | 193 | 0.60 | 0.82 | 27 | FMN, UNL |
Interfaces
1 interface between chains.
- A–B · 3112 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3M5K · Crystal structure of Putative NADH dehydrogenase/NAD(P)H nitroreductase (BDI_1728) from… · 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 A6LCR1
- Elsewhere: RCSB PDB 3M5K · PDBe 3M5K · UniProt A6LCR1
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