Research workbench

Topoisomerase iia bound to G-segment DNA

Analyse Topoisomerase iia bound to G-segment DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2RGR
Type: protein + DNA
Length: 755 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA; DNA topoisomerase 2
EC: 5.99.1.3
UniProt: P06786
Ligands: MG
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	DNA	dna	15	—	—
D	DNA	dna	19	—	—
A	DNA topoisomerase 2 (EC 5.99.1.3)	protein	721	44% helix, 16% strand	P06786

Ligands and binding sites

MG · Magnesium ion · metal · chains C, A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	779	0.84	0.87	63	empty
2	449	0.76	0.85	51	empty
3	268	0.62	0.81	29	empty
4	133	0.40	0.75	25	empty
5	106	0.37	0.74	17	empty

Interfaces

3 interfaces between chains.

D–A · 815 Å² buried · 15 hydrogen bonds · protein-nucleic
C–D · 685 Å² buried · 67 hydrogen bonds · nucleic-nucleic
C–A · 640 Å² buried · 8 hydrogen bonds · protein-nucleic

Compared structures

2RGR · Topoisomerase IIA bound to G-segment DNA · the same entry in another collection · chain C against C, TM-score 1.00
P06786 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 2 (P06786) · 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 P06786
Elsewhere: RCSB PDB 2RGR · PDBe 2RGR · UniProt P06786

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