MolNFT v1 · #46470 · protein + DNA
Structure of E. COLI topoisomerase III in complex with an 8-base single stranded oligonucleotide. frozen in glucose pH 7.0
2O5E · 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3': “Structure of E. COLI topoisomerase III in complex with an 8-base single stranded oligonucleotide. frozen in…”. X-ray diffraction, 2 ligands (TDR, CL), 13 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 2O5E
- Type
- protein + DNA
- Length
- 1,279 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
- TDR, CL
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3' | dna | 7 | — | — |
| A | DNA topoisomerase 3 (EC 5.99.1.2) | protein | 634 | 44% helix, 18% strand | P14294 |
| B | DNA topoisomerase 3 (EC 5.99.1.2) | protein | 631 | 45% helix, 18% strand | P14294 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.72 | 0.79 | 75 | empty |
| 2 | 509 | 0.71 | 0.81 | 64 | empty |
| 3 | 470 | 0.71 | 0.81 | 45 | empty |
| 4 | 376 | 0.68 | 0.81 | 50 | empty |
| 5 | 141 | 0.67 | 0.89 | 22 | empty |
Interfaces
3 interfaces between chains.
- D–B · 993 Ų buried · 21 hydrogen bonds · protein-nucleic
- C–A · 992 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 673 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2O5E · 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 0.91
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 2O5E · PDBe 2O5E · UniProt P14294
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