Research workbench
Complex of E.COLI DNA topoisomerase I with 5'-thymidine monophosphate and 3'-thymidine monophosphate
Analyse Complex of E.COLI DNA topoisomerase I with 5'-thymidine monophosphate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CY8
- Type
- protein
- Length
- 563 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
- T3P, TMP, PO4
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase I (EC 5.99.1.2) | protein | 563 | 44% helix, 20% strand | P06612 |
Ligands and binding sites
- T3P · Thymidine-3'-phosphate · ligand · chains A
- TMP · Thymidine-5'-phosphate · 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.68 | 0.78 | 64 | T3P |
| 2 | 101 | 0.64 | 0.89 | 19 | empty |
| 3 | 56 | 0.28 | 0.74 | 16 | empty |
| 4 | 65 | 0.27 | 0.72 | 17 | empty |
Compared structures
- 1CY8 · Complex of E.COLI DNA topoisomerase I with 5'-thymidine monophosphate and 3'-thymidine… · the same entry in another collection · chain A against A, TM-score 1.00
- P06612 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 1 (P06612) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 1CY8 · PDBe 1CY8 · UniProt P06612
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