MolNFT v1 · #3619 · protein
Complex of E.COLI DNA topoisomerase I with 5'PTPTPT
1CY1: “Complex of E.COLI DNA topoisomerase I with 5'PTPTPT”. X-ray diffraction, 3 ligands (TMP, THP, PO4), 5 pockets (best druggability 0.64). MolNFT v1 #3619 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1CY1
- Type
- protein
- Length
- 557 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase I
- EC
- 5.99.1.2
- UniProt
- P06612
- Ligands
- TMP, THP, PO4
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase I (EC 5.99.1.2) | protein | 557 | 45% helix, 19% strand | P06612 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · 2 copies · chains A
- THP · Thymidine-3',5'-diphosphate · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
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 | 457 | 0.64 | 0.78 | 60 | TMP |
| 2 | 88 | 0.32 | 0.73 | 21 | empty |
| 3 | 72 | 0.31 | 0.74 | 21 | empty |
| 4 | 54 | 0.30 | 0.76 | 12 | empty |
| 5 | 56 | 0.30 | 0.75 | 14 | THP |
Compared structures
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 P06612
- Elsewhere: RCSB PDB 1CY1 · PDBe 1CY1 · UniProt P06612
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