ISDA: 9RYA

Deposition Date 2025-07-14

Release Date 2026-07-22

Last Version Date 2026-07-22

Entry Detail

PDB ID:

9RYA

Keywords:

DNA BINDING PROTEIN

Title:

RAPTA-3MB (Ruthenium[II]-1,3,5-trimethylbenzene-phosphaadamantane) cancer drug binding to the nucleosome core

Biological Source:

Source Organism(s):

Xenopus laevis (Taxon ID: 8355)
Homo sapiens (Taxon ID: 9606)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.70 Å

R-Value Free:

0.27

R-Value Work:

0.21

Space Group:

P 21 21 21

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Macromolecular Entities

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Chain IDs:A, E
Chain Length:135
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:P84233 Pfam ID:PF00125

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:B, F
Chain Length:102
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:P62799 Pfam ID:PF15511

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2A
Gene (Uniprot):LOC494591
Chain IDs:C, G
Chain Length:128
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:Q6AZJ8 Pfam ID:PF00125, PF16211

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2B 1.1
Chain IDs:D, H
Chain Length:125
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:P02281 Pfam ID:PF00125

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (145-MER)
Chain IDs:I
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (145-MER)
Chain IDs:J
Chain Length:145
Number of Molecules:1
Biological Source:Homo sapiens

Ligand Molecules