Research workbench
Structural basis for the mukb-topoisomerase IV interaction
Analyse Structural basis for the mukb-topoisomerase IV interaction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MN4
- Type
- protein
- Length
- 804 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 4 subunit a; Chromosome partition protein mukb
- EC
- 5.99.1.3
- UniProt
- P0AFI2, P22523
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 4 subunit a (EC 5.99.1.3) | protein | 246 | 10% helix, 39% strand | P0AFI2 |
| C | Chromosome partition protein mukb | protein | 159 | 48% helix, 18% strand | P22523 |
| D | Chromosome partition protein mukb | protein | 154 | 45% helix, 19% strand | P22523 |
| B | DNA topoisomerase 4 subunit a (EC 5.99.1.3) | protein | 245 | 10% helix, 40% strand | P0AFI2 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.66 | 0.80 | 42 | empty |
| 2 | 394 | 0.64 | 0.78 | 28 | empty |
| 3 | 346 | 0.62 | 0.78 | 23 | empty |
| 4 | 169 | 0.46 | 0.75 | 19 | empty |
| 5 | 65 | 0.40 | 0.80 | 18 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1706 Ų buried · 37 hydrogen bonds · protein-protein
- D–B · 692 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 625 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4MN4 · Structural Basis for the MukB-topoisomerase IV Interaction · the same entry in another collection · chain B against B, TM-score 1.00
- P0AFI2 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 4 subunit a (P0AFI2) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P22523 · AlphaFold monomer V2.0 prediction for chromosome partition protein mukb (P22523) · a predicted model of the same protein · chain D against A, TM-score 0.71
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 P0AFI2
- Every structure of UniProt P22523
- Elsewhere: RCSB PDB 4MN4 · PDBe 4MN4 · UniProt P0AFI2 · UniProt P22523
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