Research workbench
NADH:qui oxidoreductase (NDH-II) from Staphylococcus aureus - holoprotein structure - 2.32 A resolution
Analyse NADH:qui oxidoreductase (NDH-II) from Staphylococcus aureus - holoprotein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NA1
- Type
- protein
- Length
- 398 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.32
- Source
- Staphylococcus aureus subsp. aureus NCTC 8325
- Molecule
- NADH dehydrogenase-like protein SAOUHSC_00878
- EC
- 1.6.99.-
- UniProt
- Q2FZV7
- Ligands
- FAD, PO4
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.32 · 1 distinct chain · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH dehydrogenase-like protein SAOUHSC_00878 (EC 1.6.99.-) | protein | 398 | 37% helix, 28% strand | Q2FZV7 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- MLI · Malonate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.81 | 0.82 | 97 | FAD |
| 2 | 74 | 0.44 | 0.81 | 15 | empty |
Compared structures
- 5NA1 · NADH:QUINONE oxidoreductase (ndh-II) from staphylococcus aureus - holoprotein structure… · the same entry in another collection · chain A against A, TM-score 1.00
- Q2FZV7 · AlphaFold monomer V2.0 prediction for NADH dehydrogenase-like protein SAOUHSC_00878… · a predicted model of the same protein · 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 Q2FZV7
- Elsewhere: RCSB PDB 5NA1 · PDBe 5NA1 · UniProt Q2FZV7
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