Research workbench
Crystal Structure of Staphylococcus pseudintermedius SbnI in complex with ADP
Analyse Crystal Structure of Staphylococcus pseudintermedius SbnI in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NR6
- Type
- protein
- Length
- 508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Staphylococcus pseudintermedius
- Molecule
- Bifunctional transcriptional regulator/O-phospho-L-serine synthase SbnI
- UniProt
- A0A166Q2C7
- Ligands
- ADP, MG
- Pockets
- 9 · best druggability 0.56
Structure
x-ray diffraction · resolution 1.9 · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bifunctional transcriptional regulator/O-phospho-L-serine synthase SbnI | protein | 254 | 33% helix, 24% strand | A0A166Q2C7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.56 | 0.76 | 42 | MG, ADP |
| 2 | 259 | 0.53 | 0.76 | 30 | MG, ADP |
| 3 | 196 | 0.50 | 0.76 | 21 | empty |
| 4 | 179 | 0.46 | 0.75 | 23 | empty |
| 5 | 76 | 0.41 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 138 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6NR6 · Crystal structure of staphylococcus pseudintermedius sbni in complex with ADP · 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 A0A166Q2C7
- Elsewhere: RCSB PDB 6NR6 · PDBe 6NR6 · UniProt A0A166Q2C7
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