4N0Z

Crystal structure of cisplatin bound to a plasmodium falciparum glutaredoxin 1 (PfGrx1)

PDB DOI: https://doi.org/10.2210/pdb4N0Z/pdb

Classification: OXIDOREDUCTASE
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-10-03 Released: 2014-10-08
Deposition Author(s): Yogavel, M., Sharma, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 ?
R-Value Free: 0.172
R-Value Work: 0.155
R-Value Observed: 0.156

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Interaction of Cisplatin with plasmodium falciparum Glutaredoxin 1

Yogavel, M., Tripathi, T., Rahlfs, S., Becker, K., Sharma, A.

To be published.

Macromolecule Content

Total Structure Weight: 13.06 kDa
Atom Count: 1,034
Modelled Residue Count: 107
Deposited Residue Count: 111
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaredoxin	A	111	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: GRX1 EC: 1.20.4.1
UniProt
Find proteins for Q9NLB2 (Plasmodium falciparum (isolate 3D7)) Explore Q9NLB2 Go to UniProtKB: Q9NLB2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NLB2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CPT Query on CPT Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	Cisplatin Cl₂ H₆ N₂ Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MPO Query on MPO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C₇ H₁₅ N O₄ S DVLFYONBTKHTER-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 ?
R-Value Free: 0.172
R-Value Work: 0.155
R-Value Observed: 0.156
Space Group: P 3₂ 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 48.4	α = 90
b = 48.4	β = 90
c = 82.612	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-10-08

Deposition Author(s):

Yogavel, M.

Sharma, A.

Revision History (Full details and data files)

Version 1.0: 2014-10-08
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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4N0Z

Crystal structure of cisplatin bound to a plasmodium falciparum glutaredoxin 1 (PfGrx1)

Interaction of Cisplatin with plasmodium falciparum Glutaredoxin 1

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)