MolNFT v1 · #3644 · protein
Crystal structure of the 30 kda fragment of E. COLI DNA topoisomerase I. hexagonal form
1CYY: “Crystal structure of the 30 kda fragment of E. COLI DNA topoisomerase I. hexagonal form”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.71). MolNFT v1 #3644 on GenesisL1: 3D structure, binding sites and pockets in…
- 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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