MolNFT v1 · #141525 · protein + DNA

Human topoisomerase II beta in complex with DNA

5ZAD · DNA topoisomerase 2-beta: “Human topoisomerase II beta in complex with DNA”. X-ray diffraction, 15 pockets (best druggability 0.82). MolNFT v1 #141525 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZAD
Type: protein + DNA
Length: 1,498 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA topoisomerase 2-beta; DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3'); DNA…
EC: 5.99.1.3
UniProt: Q02880
Pockets: 15 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	DNA topoisomerase 2-beta (EC 5.99.1.3)	protein	729	47% helix, 16% strand	Q02880
C, D	DNA (5'-D(PAPGPCPCPGPAPGPC)-3')	dna	8	—	—
F, E	DNA (5'-D(PTPGPCPAPGPCPTPCPGPGPCPT)-3')	dna	12	—	—

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	524	0.82	0.88	71	empty
2	527	0.78	0.85	66	empty
3	598	0.76	0.83	67	empty
4	247	0.76	0.90	44	empty
5	1018	0.75	0.78	72	empty

Interfaces

9 interfaces between chains.

A–B · 1388 Å² buried · 26 hydrogen bonds · protein-protein
B–E · 1135 Å² buried · 28 hydrogen bonds · protein-nucleic
A–F · 1082 Å² buried · 21 hydrogen bonds · protein-nucleic
B–D · 759 Å² buried · 12 hydrogen bonds · protein-nucleic
A–C · 757 Å² buried · 11 hydrogen bonds · protein-nucleic

Compared structures

5ZAD · Human topoisomerase II beta in complex with DNA · the same entry in another collection · chain F against F, TM-score 1.00
Q02880 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 2-beta (Q02880) · 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 Q02880
Elsewhere: RCSB PDB 5ZAD · PDBe 5ZAD · UniProt Q02880

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