MolNFT v1 · #180649 · protein

Crystal structure of the ATPase and transducer domains of DNA topoisomerase II from balamuthia mandrillaris CDC:V039: BABOON/SAN DIEGO/1986

7L6S: “Crystal structure of the ATPase and transducer domains of DNA topoisomerase II from balamuthia mandrillaris…”. X-ray diffraction, 2 ligands (ANP, MG), 3 pockets (best druggability 0.76). MolNFT v1 #180649 on GenesisL1: 3D structure…

PDB: 7L6S
Type: protein
Length: 396 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA topoisomerase II
EC: 5.6.2.2
Ligands: ANP, MG
Pockets: 3 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA topoisomerase II (EC 5.6.2.2)	protein	396	34% helix, 27% strand	—

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
MG · Magnesium ion · metal · chains A
EDO · 1,2-ethanediol · additive · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	262	0.76	0.89	44	ANP, MG
2	163	0.48	0.77	25	empty
3	94	0.45	0.80	26	EDO

Compared structures

7L6S · Crystal structure of the ATPase and transducer domains of DNA topoisomerase II from… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 7L6S · PDBe 7L6S

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