3IS5 | pdb_00003is5

Crystal structure of CDPK kinase domain from toxoplasma Gondii, TGME49_018720

PDB DOI: https://doi.org/10.2210/pdb3IS5/pdb

Classification: TRANSFERASE
Organism(s): Toxoplasma gondii ME49
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-08-25 Released: 2009-10-20
Deposition Author(s): Wernimont, A.K., Artz, J.D., Senisterra, G., MacKenzie, F., Hutchinson, A., Kozieradzki, I., Cossar, D., Bochkarev, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Hui, R., Lin, Y.H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.259 (Depositor), 0.260 (DCC)
R-Value Work:
0.218 (Depositor), 0.220 (DCC)
R-Value Observed:
0.220 (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 CDPK kinase domain from toxoplasma Gondii, TGME49_018720

Wernimont, A.K., Artz, J.D., Senisterra, G., MacKenzie, F., Hutchinson, A., Kozieradzki, I., Cossar, D., Bochkarev, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Hui, R., Lin, Y.H.

To be published.

Macromolecule Content

Total Structure Weight: 199.58 kDa
Atom Count: 12,282
Modelled Residue Count: 1,533
Deposited Residue Count: 1,710
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-dependent protein kinase	A, B, C, D, E A, B, C, D, E, F	285	Toxoplasma gondii ME49	Mutation(s): 0 Gene Names: TGME49_018720 EC: 2.7.11.17
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain V [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain V [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain V [auth E]	AA [auth F] G [auth A] L [auth B] O [auth C] R [auth D] AA [auth F], G [auth A], L [auth B], O [auth C], R [auth D], V [auth E]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain AA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain V [auth E] Interactions & Density Focus chain AA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain V [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain W [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E]	BA [auth F] I [auth A] K [auth A] N [auth B] S [auth D] BA [auth F], I [auth A], K [auth A], N [auth B], S [auth D], T [auth D], W [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain I [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain S [auth D] Focus chain T [auth D] Focus chain W [auth E] Interactions & Density Focus chain BA [auth F] Focus chain I [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain S [auth D] Focus chain T [auth D] Focus chain W [auth E]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth C] SDF format, chain Y [auth F] MOL2 format, chain H [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Y [auth F] mmCIF format, chain H [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Y [auth F]	H [auth A], P [auth C], Y [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain P [auth C] Focus chain Y [auth F] Interactions & Density Focus chain H [auth A] Focus chain P [auth C] Focus chain Y [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] SDF format, chain Z [auth F] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Z [auth F]	J [auth A] M [auth B] Q [auth C] U [auth D] X [auth E] J [auth A], M [auth B], Q [auth C], U [auth D], X [auth E], Z [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.259 (Depositor), 0.260 (DCC)
R-Value Work: 0.218 (Depositor), 0.220 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.973	α = 90
b = 113.973	β = 90
c = 153.471	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-10-20

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-10-20
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