MolNFT v1 · #75669 · protein + DNA
Crystal structure of covalent complex of topoisomerase 1A with substrate
3PX7 · DNA topoisomerase: “Crystal structure of covalent complex of topoisomerase 1A with substrate”. X-ray diffraction, 1 ligand (HG), 5 pockets (best druggability 0.69). MolNFT v1 #75669 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3PX7
- Type
- protein + DNA
- Length
- 561 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase; DNA 5'-D(*TP*TP*GP*GP*G)-3'; DNA 5'-D(*A*AP*TP*GP*CP*GP*CP*T)-3'
- EC
- 5.99.1.2
- UniProt
- C9QXS7
- Ligands
- HG
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase (EC 5.99.1.2) | protein | 552 | 44% helix, 20% strand | C9QXS7 |
| B | DNA 5'-D(*TP*TP*GP*GP*G)-3' | dna | 2 | — | — |
| C | DNA 5'-D(*A*AP*TP*GP*CP*GP*CP*T)-3' | dna | 7 | — | — |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.69 | 0.79 | 57 | empty |
| 2 | 128 | 0.39 | 0.74 | 19 | empty |
| 3 | 88 | 0.38 | 0.77 | 15 | empty |
| 4 | 51 | 0.35 | 0.79 | 11 | empty |
| 5 | 58 | 0.29 | 0.75 | 17 | HG |
Interfaces
3 interfaces between chains.
- A–C · 994 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–B · 280 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 82 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3PX7 · Crystal Structure of covalent complex of topoisomerase 1A with substrate · the same entry in another collection · 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 C9QXS7
- Elsewhere: RCSB PDB 3PX7 · PDBe 3PX7 · UniProt C9QXS7
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