MolNFT v1 · #91739 · protein + DNA

Human topoisomerase II alpha bound to DNA

4FM9 · DNA topoisomerase 2-alpha: “Human topoisomerase II alpha bound to DNA”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.79). MolNFT v1 #91739 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4FM9
Type: protein + DNA
Length: 757 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA topoisomerase 2-alpha; DNA (5'-D(P*GP*AP*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*G)-3'); DNA…
EC: 5.99.1.3
UniProt: P11388
Ligands: MG
Pockets: 8 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA topoisomerase 2-alpha (EC 5.99.1.3)	protein	727	47% helix, 13% strand	P11388
C	DNA (5'-D(PGPAPGPGPAPTPGPAPCPGPAPTP*G)-3')	dna	13	—	—
D	DNA (5'- D(CPGPCPGPCPAPTPCPGPTPCPAPTPCPCPTP*C)-3')	dna	17	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, C, D
GOL · Glycerol · additive · chains A

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1025	0.79	0.81	75	GOL
2	1110	0.77	0.80	73	MG
3	626	0.77	0.83	41	empty
4	166	0.62	0.84	23	empty
5	297	0.62	0.79	39	empty

Interfaces

3 interfaces between chains.

A–D · 864 Å² buried · 27 hydrogen bonds · protein-nucleic
A–C · 789 Å² buried · 10 hydrogen bonds · protein-nucleic
C–D · 571 Å² buried · 58 hydrogen bonds · nucleic-nucleic

Compared structures

4FM9 · Human topoisomerase II alpha bound to DNA · the same entry in another collection · chain A against A, TM-score 1.00
P11388 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 2-alpha (P11388) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P11388
Elsewhere: RCSB PDB 4FM9 · PDBe 4FM9 · UniProt P11388

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