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Structure of cpii, a nitrogen regulatory pii-like protein from thiomonas intermedia K12, bound to ADP, AMP and bicarbonate.
Analyse Structure of cpii, a nitrogen regulatory pii-like protein from thiomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D4O
- Type
- protein
- Length
- 300 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogen regulatory protein P-II
- UniProt
- D5X329
- Ligands
- BCT, ADP, AMP
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogen regulatory protein P-II | protein | 106 | 38% helix, 40% strand | D5X329 |
| B | Nitrogen regulatory protein P-II | protein | 90 | 34% helix, 49% strand | D5X329 |
| C | Nitrogen regulatory protein P-II | protein | 104 | 32% helix, 40% strand | D5X329 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, B, C
- ADP · Adenosine-5'-diphosphate · ligand · chains A, C
- AMP · Adenosine monophosphate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.70 | 0.91 | 25 | ADP |
| 2 | 131 | 0.69 | 0.90 | 21 | AMP |
| 3 | 297 | 0.64 | 0.80 | 40 | empty |
| 4 | 89 | 0.60 | 0.88 | 16 | BCT |
| 5 | 62 | 0.49 | 0.85 | 16 | BCT |
Interfaces
3 interfaces between chains.
- A–B · 921 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 878 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 860 Ų buried · 17 hydrogen bonds · protein-protein
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 5D4O · PDBe 5D4O · UniProt D5X329
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