3MNN

A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A ruthenium antimetastasis agent forms specific histone protein adducts in the nucleosome core

Wu, B.Ong, M.S.Groessl, M.Adhireksan, Z.Hartinger, C.G.Dyson, P.J.Davey, C.A.

(2011) Chemistry 17: 3562-3566


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E
135Xenopus laevisMutation(s): 0 
Gene Names: HISTONE H3
UniProt
Find proteins for P84233 (Xenopus laevis)
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Go to UniProtKB:  P84233
Entity Groups  
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UniProt GroupP84233
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
102Xenopus laevisMutation(s): 0 
Gene Names: HISTONE H4
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
119Xenopus laevisMutation(s): 0 
Gene Names: HISTONE H2ALOC494591
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1
D, H
125Xenopus laevisMutation(s): 0 
Gene Names: HISTONE H2B
UniProt
Find proteins for P02281 (Xenopus laevis)
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UniProt GroupP02281
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (145-MER)145N/A
Sequence Annotations
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (145-MER)145N/A
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PTW
Query on PTW

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O [auth F],
S [auth G],
W [auth H]
1,3,5-triaza-7-phosphatricyclo[3.3.1.1~3,7~]decane
C6 H12 N3 P
FXXRPTKTLVHPAR-UHFFFAOYSA-N
MML
Query on MML

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N [auth F],
R [auth G],
V [auth H]
1-methyl-4-(1-methylethyl)benzene
C10 H14
HFPZCAJZSCWRBC-UHFFFAOYSA-N
RU
Query on RU

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M [auth F],
Q [auth G],
U [auth H]
RUTHENIUM ION
Ru
BPEVHDGLPIIAGH-UHFFFAOYSA-N
SO4
Query on SO4

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K [auth D],
P [auth G],
T [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
Query on MG

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L [auth E]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.35α = 90
b = 109.86β = 90
c = 182.59γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
PHASESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description