2PML | pdb_00002pml

Crystal structure of PfPK7 in complex with an ATP analogue

PDB DOI: https://doi.org/10.2210/pdb2PML/pdb

Classification: TRANSFERASE
Organism(s): Plasmodium falciparum
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2007-04-23 Released: 2008-01-22
Deposition Author(s): Merckx, A., Echalier, A., Noble, M., Endicott, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.327 (Depositor), 0.312 (DCC)
R-Value Work:
0.258 (Depositor), 0.248 (DCC)
R-Value Observed:
0.261 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Structures of PfPK7 an atypical protein kinase from P. falciparum identify a novel activation motif and leads for inhibitor design

Merckx, A., Echalier, A., Langford, K., Sicard, A., Langsley, G., Joore, J., Doerig, C., Noble, M., Endicott, J.

To be published.

Macromolecule Content

Total Structure Weight: 42 kDa
Atom Count: 2,927
Modeled Residue Count: 340
Deposited Residue Count: 348
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ser/Thr protein kinase	A [auth X]	348	Plasmodium falciparum	Mutation(s): 0 Gene Names: PFB0605w EC: 2.7.12.2
UniProt
Find proteins for O96214 (Plasmodium falciparum) Explore O96214 Go to UniProtKB: O96214
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O96214
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	C [auth X]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.327 (Depositor), 0.312 (DCC)
R-Value Work: 0.258 (Depositor), 0.248 (DCC)
R-Value Observed: 0.261 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.554	α = 90
b = 81.795	β = 90
c = 138.273	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DNA	data collection
MOSFLM	data reduction
SCALA	data scaling
SHELXS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-01-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-01-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.