MolNFT v1 · #9789 · protein + DNA
Noncovalent complex of E.COLI DNA topoisomerase III with an 8-base single-stranded DNA oligonucleotide
1I7D · 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3': “Noncovalent complex of E.COLI DNA topoisomerase III with an 8-base single-stranded DNA oligonucleotide”. X-ray diffraction, 2 ligands (CL, SO4), 7 pockets (best druggability 0.63). MolNFT v1 #9789…
- PDB
- 1I7D
- Type
- protein + DNA
- Length
- 628 residues
- Chains
- 2
- 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 III
- EC
- 5.99.1.2
- UniProt
- P14294
- Ligands
- CL, SO4
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3' | dna | 8 | — | — |
| A | DNA topoisomerase III (EC 5.99.1.2) | protein | 620 | 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.63 | 0.80 | 37 | empty |
| 2 | 283 | 0.63 | 0.81 | 33 | empty |
| 3 | 252 | 0.58 | 0.79 | 40 | empty |
| 4 | 168 | 0.42 | 0.74 | 36 | empty |
| 5 | 137 | 0.41 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- B–A · 1270 Ų buried · 30 hydrogen bonds · protein-nucleic
Compared structures
- 1I7D · Noncovalent complex of E.COLI DNA topoisomerase III with an 8-base single-stranded DNA… · the same entry in another collection · chain B against B, TM-score 1.00
- P14294 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 3 (P14294) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 1I7D · PDBe 1I7D · UniProt P14294
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