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Breakage-reunion domain of S.PNEUMONIAE topo IV: crystal structure of a gram-positive quinolone target
Analyse Breakage-reunion domain of S.PNEUMONIAE topo IV: crystal structure of a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NOV
- Type
- protein
- Length
- 1,782 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 4 subunit a
- EC
- 5.99.1.-
- UniProt
- P72525
- Pockets
- 13 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 4 subunit a (EC 5.99.1.-) | protein | 440 | 45% helix, 13% strand | P72525 |
| B | DNA topoisomerase 4 subunit a (EC 5.99.1.-) | protein | 451 | 43% helix, 13% strand | P72525 |
| C | DNA topoisomerase 4 subunit a (EC 5.99.1.-) | protein | 451 | 43% helix, 13% strand | P72525 |
| D | DNA topoisomerase 4 subunit a (EC 5.99.1.-) | protein | 440 | 40% helix, 11% strand | P72525 |
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.66 | 0.83 | 34 | empty |
| 2 | 81 | 0.62 | 0.89 | 22 | empty |
| 3 | 180 | 0.51 | 0.77 | 28 | empty |
| 4 | 128 | 0.49 | 0.79 | 22 | empty |
| 5 | 164 | 0.47 | 0.76 | 29 | empty |
Interfaces
2 interfaces between chains.
- C–D · 1477 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1464 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 2NOV · Breakage-reunion domain of S.pneumoniae topo IV: crystal structure of a gram-positive… · the same entry in another collection · chain D against D, TM-score 1.00
- P72525 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 4 subunit a (P72525) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P72525
- Elsewhere: RCSB PDB 2NOV · PDBe 2NOV · UniProt P72525
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