3IWL | pdb_00003iwl

Crystal structure of cisplatin bound to a human copper chaperone (monomer)

• PDB DOI: https://doi.org/10.2210/pdb3IWL/pdb

• Classification: METAL TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-02 Released: 2009-09-22 
• Deposition Author(s): Boal, A.K., Rosenzweig, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 4YDX

Literature

Crystal structures of cisplatin bound to a human copper chaperone.

Boal, A.K., Rosenzweig, A.C.

(2009) J Am Chem Soc 131: 14196-14197

• PubMed: 19807176 
• DOI: https://doi.org/10.1021/ja906363t
• Primary Citation Related Structures: 
  3IWL, 3IWX


• PubMed Abstract: 
  

  Copper trafficking proteins, including the chaperone Atox1 and the P(1B)-type ATPase ATP7B, have been implicated in cellular resistance to the anticancer drug cisplatin. We have determined two crystal structures of cisplatin-Atox1 adducts that reveal platinum coordination by the conserved CXXC copper-binding motif. Direct interaction of cisplatin with this functionally relevant site has significant implications for understanding the molecular basis for resistance mediated by copper transport pathways.

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Organizational Affiliation: 
• Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 7.95 kDa 
• Atom Count: 609 
• Modeled Residue Count: 66 
• Deposited Residue Count: 68 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper transport protein ATOX1	A	68	Homo sapiens	Mutation(s): 0  Gene Names: ATOX1, HAH1
UniProt & NIH Common Fund Data Resources
Find proteins for O00244 (Homo sapiens) Explore O00244  Go to UniProtKB:  O00244
PHAROS:  O00244 GTEx:  ENSG00000177556

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TCE	D [auth A]	3,3',3''-phosphanetriyltripropanoic acid C9 H15 O6 P PZBFGYYEXUXCOF-UHFFFAOYSA-N
PT	B [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.07	α = 90
b = 54.07	β = 90
c = 55.578	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Boal, A.K., Rosenzweig, A.C.

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations