MolNFT v1 · #142045 · protein + DNA

Crystal structure of human topoisomerase II beta in complex with 5- iodouridine-containing-DNA and etoposide in space group P21

5ZRF: “Crystal structure of human topoisomerase II beta in complex with 5- iodouridine-containing-DNA and etoposide…”. X-ray diffraction, 2 ligands (EVP, MG). MolNFT v1 #142045 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZRF
Type: protein + DNA
Length: 1,380 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: Q02880
Ligands: EVP, MG

Structure

x-ray diffraction · 4 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	669	—	Q02880
B	—	protein	671	—	Q02880
C, E	—	dna	8	—	—
D, F	—	dna	12	—	—

Ligands and binding sites

EVP · (5s,5ar,8ar,9r)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5A,6,8,8A,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol-5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside · ligand · 2 copies · chains B, D, E, F, A, C
MG · Magnesium ion · metal · 6 copies · chains A, B

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

Compared structures

5ZRF · Crystal structure of human topoisomerase II beta in complex with… · 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 0.97

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 Q02880
Elsewhere: RCSB PDB 5ZRF · PDBe 5ZRF · UniProt Q02880

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