Research workbench
Staphylopine dehydrogenase (SaODH) - NADP+ bound
Analyse Staphylopine dehydrogenase (SaODH) - NADP+ bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C4T
- Type
- protein
- Length
- 428 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.49
- Source
- Staphylococcus aureus
- Molecule
- Staphylopine dehydrogenase
- UniProt
- A0A1Q4GXD5
- Ligands
- NA7
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.49 · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Staphylopine dehydrogenase | protein | 428 | 45% helix, 16% strand | A0A1Q4GXD5 |
Ligands and binding sites
- NA7 · [(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxy-4-(phosphonooxy)tetrahydrofuran-2-yl]methyl [(2R,3S,4S)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.80 | 0.93 | 27 | empty |
| 2 | 1128 | 0.77 | 0.79 | 95 | NA7 |
| 3 | 58 | 0.26 | 0.72 | 17 | empty |
Compared structures
- 6C4T · Staphylopine dehydrogenase (saodh) - NADP+ bound · 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 A0A1Q4GXD5
- Elsewhere: RCSB PDB 6C4T · PDBe 6C4T · UniProt A0A1Q4GXD5
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