3PM8 | pdb_00003pm8

CAD domain of PFF0520w, Calcium dependent protein kinase

PDB DOI: https://doi.org/10.2210/pdb3PM8/pdb

Classification: TRANSFERASE
Organism(s): Plasmodium falciparum K1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-11-16 Released: 2010-12-08
Deposition Author(s): Wernimont, A.K., Hutchinson, A., Lew, J., Chamberlain, K., MacKenzie, F., Loppnau, P., Cossar, D., Crombet, L., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Hui, R., Amani, M., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.225 (Depositor), 0.233 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

CAD domain of PFF0520w, Calcium dependent protein kinase

Wernimont, A.K., Hutchinson, A., Lew, J., Chamberlain, K., MacKenzie, F., Loppnau, P., Cossar, D., Crombet, L., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Hui, R., Amani, M.

To be published.

Macromolecule Content

Total Structure Weight: 45.61 kDa
Atom Count: 2,769
Modeled Residue Count: 339
Deposited Residue Count: 394
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-dependent protein kinase 2	A, B	197	Plasmodium falciparum K1	Mutation(s): 0 Gene Names: CPK2, CDPK2 EC: 2.7.11.1
UniProt
Find proteins for O15865 (Plasmodium falciparum (isolate K1 / Thailand)) Explore O15865 Go to UniProtKB: O15865
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15865
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	C [auth A] D [auth A] E [auth A] H [auth B] I [auth B] C [auth A], D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B]	G [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	F [auth A], K [auth B], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.225 (Depositor), 0.233 (DCC)
R-Value Work: 0.199 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.019	α = 68.53
b = 51.378	β = 65.75
c = 51.639	γ = 64.49

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-12-08

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-12-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2018-01-24
Changes: Structure summary
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description