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Structure of E. COLI topoisomerase III in complex with an 8-base single stranded oligonucleotide. frozen in glycerol pH 8.0
Analyse Structure of E. COLI topoisomerase III in complex with an 8-base single… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O59
- Type
- protein + DNA
- Length
- 1,260 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3'; DNA topoisomerase 3
- EC
- 5.99.1.2
- UniProt
- P14294
- Ligands
- CL
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3' | dna | 7 | — | — |
| D | 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3' | dna | 8 | — | — |
| A | DNA topoisomerase 3 (EC 5.99.1.2) | protein | 619 | 44% helix, 19% strand | P14294 |
| B | DNA topoisomerase 3 (EC 5.99.1.2) | protein | 626 | 44% helix, 18% strand | P14294 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.81 | 0.83 | 127 | empty |
| 2 | 580 | 0.72 | 0.80 | 50 | empty |
| 3 | 508 | 0.69 | 0.79 | 68 | empty |
| 4 | 325 | 0.65 | 0.81 | 38 | empty |
| 5 | 311 | 0.62 | 0.79 | 40 | empty |
Interfaces
3 interfaces between chains.
- D–B · 1240 Ų buried · 27 hydrogen bonds · protein-nucleic
- C–A · 934 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 600 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2O59 · Structure of E. coli topoisomerase III in complex with an 8-base single stranded… · the same entry in another collection · chain C against C, TM-score 1.00
- P14294 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 3 (P14294) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P14294
- Elsewhere: RCSB PDB 2O59 · PDBe 2O59 · UniProt P14294
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