Research workbench
Crystal structure of the yhdh oxidoreductase from salmonella enterica in complex with NADP
Analyse Crystal structure of the yhdh oxidoreductase from salmonella enterica in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NX4
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative oxidoreductase
- UniProt
- Q7CPM2
- Ligands
- NAP
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative oxidoreductase | protein | 324 | 35% helix, 29% strand | Q7CPM2 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.77 | 0.83 | 65 | NAP |
| 2 | 631 | 0.77 | 0.83 | 66 | NAP |
| 3 | 106 | 0.47 | 0.80 | 18 | empty |
| 4 | 121 | 0.45 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1253 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3NX4 · Crystal structure of the yhdH oxidoreductase from Salmonella enterica in complex with NADP · 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 Q7CPM2
- Elsewhere: RCSB PDB 3NX4 · PDBe 3NX4 · UniProt Q7CPM2
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