3IED | pdb_00003ied

Crystal structure of N-terminal domain of Plasmodium falciparum Hsp90 (PF14_0417) in complex with AMPPN

PDB DOI: https://doi.org/10.2210/pdb3IED/pdb

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

Deposited: 2009-07-22 Released: 2009-08-25
Deposition Author(s): Pizarro, J.C., Wernimont, A.K., Lew, J., Hutchinson, A., Artz, J.D., Amaya, M.F., Plotnikova, O., Vedadi, M., Kozieradzki, I., Weigelt, J., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Botchkarev, A., Hui, R., Hills, T., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.273 (Depositor), 0.272 (DCC)
R-Value Work:
0.232 (Depositor), 0.234 (DCC)
R-Value Observed:
0.234 (Depositor)

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

Crystal structure of N-terminal domain of Plasmodium falciparum Hsp90 (PF14_0417) in complex with AMPPN

Pizarro, J.C., Wernimont, A.K., Lew, J., Hutchinson, A., Artz, J.D., Amaya, M.F., Plotnikova, O., Vedadi, M., Kozieradzki, I., Weigelt, J., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Botchkarev, A., Hui, R., Hills, T., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 31.93 kDa
Atom Count: 1,966
Modeled Residue Count: 224
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein	A	272	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PF14_0417
UniProt
Find proteins for Q8IL32 (Plasmodium falciparum (isolate 3D7)) Explore Q8IL32 Go to UniProtKB: Q8IL32
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IL32
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AN2 Query on AN2 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]	AMP PHOSPHORAMIDATE C₁₀ H₁₆ N₆ O₉ P₂ FQMDCEJHLOLKLI-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.273 (Depositor), 0.272 (DCC)
R-Value Work: 0.232 (Depositor), 0.234 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.236	α = 90
b = 69.462	β = 90
c = 71.382	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-08-25

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-08-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description