MolNFT v1 · #3621 · protein

Complex of E.COLI DNA topoisomerase I with 5'PTPTPTP3'

1CY4: “Complex of E.COLI DNA topoisomerase I with 5'PTPTPTP3'”. X-ray diffraction, 2 ligands (TMP, PO4), 5 pockets (best druggability 0.68). MolNFT v1 #3621 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1CY4
Type: protein
Length: 558 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 0.68

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA topoisomerase I (EC 5.99.1.2)	protein	558	44% helix, 19% strand	P06612

Ligands and binding sites

TMP · Thymidine-5'-phosphate · ligand · chains A
PO4 · Phosphate ion · ion · 3 copies · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	549	0.68	0.78	71	TMP
2	90	0.63	0.89	18	empty
3	70	0.32	0.75	20	empty
4	67	0.28	0.73	16	empty
5	54	0.27	0.74	11	empty

Compared structures

1CY4 · COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'pTpTpTp3' · 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 1CY4 · PDBe 1CY4 · UniProt P06612

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.