MolNFT v1 · #106280 · protein + DNA
Crystal structure of full-length E.COLI topoisomerase I in complex with ssdna
4RUL · DNA topoisomerase 1: “Crystal structure of full-length E.COLI topoisomerase I in complex with ssdna”. X-ray diffraction, 2 ligands (ZN, SO4), 11 pockets (best druggability 0.67). MolNFT v1 #106280 on GenesisL1: 3D structure, binding…
- PDB
- 4RUL
- Type
- protein + DNA
- Length
- 836 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 1; Single strand DNA
- EC
- 5.99.1.2
- UniProt
- C9QXS7
- Ligands
- ZN, SO4
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 1 (EC 5.99.1.2) | protein | 823 | 32% helix, 25% strand | C9QXS7 |
| B | Single strand DNA | dna | 13 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.67 | 0.79 | 52 | empty |
| 2 | 347 | 0.67 | 0.81 | 43 | empty |
| 3 | 553 | 0.67 | 0.77 | 60 | SO4 |
| 4 | 170 | 0.62 | 0.84 | 23 | SO4 |
| 5 | 135 | 0.58 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1535 Ų buried · 23 hydrogen bonds · protein-nucleic
Compared structures
- 4RUL · Crystal structure of full-length E.Coli topoisomerase I in complex with ssDNA · 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 4RUL · PDBe 4RUL · UniProt C9QXS7
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