Research workbench
PII-like SbtB from Cyanobium sp PCC 7001 bound to ATP
Analyse PII-like SbtB from Cyanobium sp PCC 7001 bound to ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NTB
- Type
- protein
- Length
- 297 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Cyanobium sp. PCC 7001
- Molecule
- SbtB7001, PII-like protein
- UniProt
- B5II98
- Ligands
- ATP, CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · resolution 1.9 · 3 distinct chains · 29% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SbtB7001, PII-like protein | protein | 95 | 31% helix, 40% strand | B5II98 |
| B | SbtB7001, PII-like protein | protein | 98 | 30% helix, 39% strand | B5II98 |
| C | SbtB7001, PII-like protein | protein | 104 | 28% helix, 38% strand | B5II98 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 3 copies · chains A, C, B
- CL · Chloride ion · ion · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.73 | 0.93 | 27 | ATP |
| 2 | 125 | 0.69 | 0.91 | 28 | ATP |
| 3 | 125 | 0.68 | 0.90 | 26 | ATP |
| 4 | 65 | 0.40 | 0.80 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 995 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 963 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 839 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6NTB · Pii-like sbtb from cyanobium sp pcc 7001 bound to ATP · 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 B5II98
- Elsewhere: RCSB PDB 6NTB · PDBe 6NTB · UniProt B5II98
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