MolNFT v1 · #116907 · protein
2.0 a structure of cpii, a nitrogen regulatory pii-like protein from thiomonas intermedia K12, bound AMP
5DS7 · Nitrogen regulatory protein P-II: “2.0 a structure of cpii, a nitrogen regulatory pii-like protein from thiomonas intermedia K12, bound AMP”. X-ray diffraction, 2 ligands (AMP, CL), 6 pockets (best druggability 0.73). MolNFT v1…
- PDB
- 5DS7
- Type
- protein
- Length
- 290 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, CL
- Pockets
- 6 · best druggability 0.73
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 | 91 | 31% helix, 51% strand | D5X329 |
| B | Nitrogen regulatory protein P-II | protein | 105 | 38% helix, 36% strand | D5X329 |
| C | Nitrogen regulatory protein P-II | protein | 94 | 36% helix, 44% strand | D5X329 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains A, C, B
- CL · Chloride ion · ion · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.73 | 0.93 | 24 | AMP |
| 2 | 134 | 0.68 | 0.89 | 26 | AMP |
| 3 | 342 | 0.65 | 0.80 | 41 | AMP |
| 4 | 93 | 0.60 | 0.87 | 16 | CL |
| 5 | 172 | 0.53 | 0.79 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 919 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 786 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 765 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5DS7 · 2.0 A Structure of CPII, a nitrogen regulatory PII-like protein from Thiomonas intermedia… · 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 5DS7 · PDBe 5DS7 · UniProt D5X329
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