MolNFT v1 · #116885 · protein
2.3 ångström structure of cpii, a nitrogen regulatory pii-like protein from thiomonas intermedia K12, bound to ADP, AMP and bicarbonate.
5DRK · Nitrogen regulatory protein P-II: “2.3 ångström structure of cpii, a nitrogen regulatory pii-like protein from thiomonas intermedia K12, bound…”. X-ray diffraction, 3 ligands (AMP, ADP, BCT), 5 pockets (best druggability 0.70).…
- PDB
- 5DRK
- Type
- protein
- Length
- 283 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogen regulatory protein P-II
- UniProt
- D5X329
- Ligands
- AMP, ADP, BCT
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogen regulatory protein P-II | protein | 89 | 31% helix, 42% strand | D5X329 |
| B | Nitrogen regulatory protein P-II | protein | 105 | 38% helix, 39% strand | D5X329 |
| C | Nitrogen regulatory protein P-II | protein | 89 | 38% helix, 42% strand | D5X329 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains B, C
- BCT · Bicarbonate ion · ligand · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.70 | 0.90 | 23 | AMP |
| 2 | 138 | 0.66 | 0.88 | 25 | ADP |
| 3 | 87 | 0.58 | 0.86 | 17 | BCT |
| 4 | 171 | 0.58 | 0.81 | 17 | empty |
| 5 | 140 | 0.40 | 0.73 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 887 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 782 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 683 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5DRK · 2.3 Angstrom Structure of CPII, a nitrogen regulatory PII-like protein from Thiomonas… · 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 D5X329
- Elsewhere: RCSB PDB 5DRK · PDBe 5DRK · UniProt D5X329
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