2WTF | pdb_00002wtf

DNA polymerase eta in complex with the cis-diammineplatinum (II) 1,3- GTG intrastrand cross-link

• PDB DOI: https://doi.org/10.2210/pdb2WTF/pdb
• NAKB: 2WTF

• Classification: TRANSFERASE/DNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-16 Released: 2010-03-31 
• Deposition Author(s): Reissner, T., Schneider, S., Ziv, O., Schorr, S., Livneh, Z., Carell, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.269 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Cisplatin-(1,3-Gtg) Cross-Link within DNA Polymerase Eta.

Reissner, T., Schneider, S., Schorr, S., Carell, T.

(2010) Angew Chem Int Ed Engl 49: 3077

• PubMed: 20333640 
• DOI: https://doi.org/10.1002/anie.201000414
• Primary Citation Related Structures: 
  2WTF

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Organizational Affiliation: 
• Center for Integrated Protein Science (CiPSM), Department of Chemistry, Ludwig-Maximilians-University, Butenandtstrasse 5-13, 81377 Munich, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 139.2 kDa 
• Atom Count: 9,100 
• Modeled Residue Count: 1,061 
• Deposited Residue Count: 1,124 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA POLYMERASE ETA	A, B	536	Saccharomyces cerevisiae	Mutation(s): 0  EC: 2.7.7.7
UniProt
Find proteins for Q04049 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04049  Go to UniProtKB:  Q04049

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*CP*TP*TP*CP*TP*GP*TP*GP*CP *TP*CP*AP*CP*CP*AP*CP)-3'	C [auth O], E [auth S]	17	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*GP*TP*GP*GP*TP*GP*AP*GP*CP)-3'	D [auth P], F [auth T]	9	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTP	G [auth A], N [auth B]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C10 H16 N5 O12 P3 SUYVUBYJARFZHO-RRKCRQDMSA-N
CPT	S [auth O], T [auth S]	Cisplatin Cl2 H6 N2 Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L
CA	H [auth A], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.269 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.24	α = 90
b = 103.24	β = 90
c = 292.74	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHASER	phasing
SHARP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-31 
Deposition Author(s): Reissner, T., Schneider, S., Ziv, O., Schorr, S., Livneh, Z., Carell, T.

Revision History  

• Version 1.0: 2010-03-31
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description