Research workbench
The crystal structure of bacillus subtilis ypgq in complex with ADP
Analyse The crystal structure of bacillus subtilis ypgq 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
- 5DQW
- Type
- protein
- Length
- 371 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- A0A0D5CVW2
- Ligands
- ADP, NI
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 188 | 73% helix, 0% strand | A0A0D5CVW2 |
| B | Uncharacterized protein | protein | 183 | 70% helix, 0% strand | A0A0D5CVW2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 477 | 0.67 | 0.79 | 47 | ADP, NI |
| 2 | 388 | 0.61 | 0.77 | 45 | ADP, NI |
| 3 | 92 | 0.42 | 0.78 | 19 | empty |
| 4 | 100 | 0.40 | 0.77 | 21 | empty |
| 5 | 67 | 0.31 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1216 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5DQW · The crystal structure of Bacillus subtilis YpgQ 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 A0A0D5CVW2
- Elsewhere: RCSB PDB 5DQW · PDBe 5DQW · UniProt A0A0D5CVW2
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