Research workbench
Complex of E.COLI DNA topoisomerase I with 5'-thymidine monophosphate
Analyse Complex of E.COLI DNA topoisomerase I with 5'-thymidine monophosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CY7
- 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
- TMP, PO4
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase I (EC 5.99.1.2) | protein | 563 | 44% helix, 18% strand | P06612 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.65 | 0.79 | 53 | TMP |
| 2 | 101 | 0.63 | 0.88 | 18 | empty |
| 3 | 421 | 0.62 | 0.77 | 60 | empty |
| 4 | 70 | 0.30 | 0.73 | 20 | empty |
| 5 | 56 | 0.29 | 0.74 | 13 | TMP |
Compared structures
- 1CY7 · Complex of E.COLI DNA topoisomerase I with 5'-thymidine monophosphate · 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 1CY7 · PDBe 1CY7 · UniProt P06612
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