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Dimerization of E. COLI DNA gyrase B provides a structural mechanism for activating the ATPase catalytic center
Analyse Dimerization of E. COLI DNA gyrase B provides a structural mechanism for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EI1
- Type
- protein
- Length
- 782 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase B
- EC
- 5.99.1.3
- UniProt
- P06982
- Ligands
- ANP, SO4
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA gyrase B (EC 5.99.1.3) | protein | 391 | 37% helix, 25% strand | P06982 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.83 | 0.97 | 39 | ANP, GOL |
| 2 | 191 | 0.83 | 0.97 | 42 | ANP, GOL |
| 3 | 784 | 0.72 | 0.78 | 82 | empty |
| 4 | 207 | 0.54 | 0.78 | 21 | empty |
| 5 | 53 | 0.37 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2930 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 1EI1 · Dimerization of E. COLI DNA gyrase B provides a structural mechanism for activating the… · 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 P06982
- Elsewhere: RCSB PDB 1EI1 · PDBe 1EI1 · UniProt P06982
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