Research workbench
Crystal structure of the 30 kda fragment of E. COLI DNA topoisomerase I. hexagonal form
Analyse Crystal structure of the 30 kda fragment of E. COLI DNA topoisomerase I.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CYY
- Type
- protein
- Length
- 501 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase I
- EC
- 5.99.1.2
- UniProt
- P06612
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase I (EC 5.99.1.2) | protein | 250 | 32% helix, 30% strand | P06612 |
| B | DNA topoisomerase I (EC 5.99.1.2) | protein | 251 | 31% helix, 29% strand | P06612 |
Ligands and binding sites
- ZN · Zinc ion · metal · 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 | 876 | 0.71 | 0.76 | 66 | empty |
| 2 | 58 | 0.43 | 0.83 | 16 | empty |
| 3 | 183 | 0.42 | 0.73 | 30 | empty |
| 4 | 72 | 0.32 | 0.75 | 18 | empty |
| 5 | 59 | 0.28 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1542 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1CYY · Crystal structure of the 30 kda fragment of E. COLI DNA topoisomerase I. hexagonal form · 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 B against A, TM-score 0.84
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 1CYY · PDBe 1CYY · UniProt P06612
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