2WTF

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.269 (Depositor), 0.270 (DCC)
R-Value Work:
0.227 (Depositor), 0.230 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/anie.201000414
Primary Citation of Related Structures:
2WTF

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q04049
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(TPCPTPTPCPTPGPTPGPCP TPCPAPCPCPAP*CP)-3'	C [auth O], E [auth S]	17	N/A
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(GPTPGPGPTPGPAPGP*CP)-3'	D [auth P], F [auth T]	9	N/A
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DTP Query on DTP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B]	G [auth A], N [auth B]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₂ P₃ SUYVUBYJARFZHO-RRKCRQDMSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth B]
CPT Query on CPT Download Ideal Coordinates CCD File SDF format, chain T [auth S] SDF format, chain S [auth O] MOL2 format, chain T [auth S] MOL2 format, chain S [auth O] mmCIF format, chain T [auth S] mmCIF format, chain S [auth O]	S [auth O], T [auth S]	Cisplatin Cl₂ H₆ N₂ Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L		Interactions Focus chain S [auth O] Focus chain T [auth S] Interactions & Density Focus chain S [auth O] Focus chain T [auth S]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth B] 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		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.269 (Depositor), 0.270 (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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-03-31

Deposition Author(s):

Revision History (Full details and data files)

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