MolNFT v1 · #61952 · protein
Crystal structure of putative NADH oxidase (NP_348178.1) from clostridium acetobutylicum at 1.40 a resolution
3E10: “Crystal structure of putative NADH oxidase (NP_348178.1) from clostridium acetobutylicum at 1.40 a resolution”. X-ray diffraction, 1 ligand (FMN), 3 pockets (best druggability 0.58). MolNFT v1 #61952 on GenesisL1: 3D structure…
- PDB
- 3E10
- Type
- protein
- Length
- 333 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative NADH oxidase
- UniProt
- Q97IT9
- Ligands
- FMN
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative NADH oxidase | protein | 166 | 43% helix, 22% strand | Q97IT9 |
| B | Putative NADH oxidase | protein | 167 | 42% helix, 22% strand | Q97IT9 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.58 | 0.81 | 28 | FMN, EDO |
| 2 | 178 | 0.57 | 0.81 | 29 | FMN, EDO, EPE |
| 3 | 163 | 0.52 | 0.78 | 26 | EDO |
Interfaces
1 interface between chains.
- A–B · 2707 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 3E10 · Crystal structure of Putative NADH Oxidase (NP_348178.1) from CLOSTRIDIUM ACETOBUTYLICUM… · 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 Q97IT9
- Elsewhere: RCSB PDB 3E10 · PDBe 3E10 · UniProt Q97IT9
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