Research workbench
Structure of cpii bound to ADP and bicarbonate, from thiomonas intermedia K12
Analyse Structure of cpii bound to ADP and bicarbonate, from thiomonas intermedia K12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D4P
- Type
- protein
- Length
- 312 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative nitrogen regulatory protein P-II glnb
- UniProt
- D5X329
- Ligands
- BCT, ADP
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative nitrogen regulatory protein P-II glnb | protein | 102 | 33% helix, 37% strand | D5X329 |
| B | Putative nitrogen regulatory protein P-II glnb | protein | 104 | 36% helix, 38% strand | D5X329 |
| C | Putative nitrogen regulatory protein P-II glnb | protein | 106 | 33% helix, 38% strand | D5X329 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 7 copies · chains A, B, C
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.71 | 0.91 | 25 | ADP |
| 2 | 127 | 0.70 | 0.91 | 24 | ADP |
| 3 | 143 | 0.68 | 0.88 | 25 | ADP |
| 4 | 106 | 0.56 | 0.84 | 17 | BCT |
| 5 | 257 | 0.56 | 0.78 | 47 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1032 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 917 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 864 Ų buried · 12 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 5D4P · PDBe 5D4P · UniProt D5X329
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