Research workbench
Aquifex aeolicus type iia topoisomerase C-terminal domain
Analyse Aquifex aeolicus type iia topoisomerase C-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NO0
- Type
- protein
- Length
- 828 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit a
- EC
- 5.99.1.3
- UniProt
- O67108
- Ligands
- NO3
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | DNA gyrase subunit a (EC 5.99.1.3) | protein | 276 | 8% helix, 46% strand | O67108 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 9 copies · chains A, B, C
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 | 709 | 0.74 | 0.79 | 56 | GOL |
| 2 | 582 | 0.73 | 0.80 | 54 | GOL |
| 3 | 583 | 0.73 | 0.80 | 57 | GOL |
| 4 | 349 | 0.58 | 0.76 | 58 | empty |
| 5 | 216 | 0.44 | 0.73 | 21 | GOL |
Interfaces
2 interfaces between chains.
- B–C · 392 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 237 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 O67108
- Elsewhere: RCSB PDB 3NO0 · PDBe 3NO0 · UniProt O67108
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