6AQE | pdb_00006aqe

Crystal structure of PPK2 in complex with Mg ATP

PDB DOI: https://doi.org/10.2210/pdb6AQE/pdb

Classification: TRANSFERASE
Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2017-08-19 Released: 2019-01-16
Deposition Author(s): Nocek, B., Joachimiak, A., Yakunin, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.186 (Depositor), 0.187 (DCC)
R-Value Work:
0.162 (Depositor), 0.163 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases

Nocek, B.P., Khusnutdinova, A.N., Ruszkowski, M., Flick, R., Burda, M., Batyrova, K., Brown, G., Mucha, A., Joachimiak, A., Berlicki, L., Yakunin, A.F.

(2018) ACS Catal 8: 10746-10760

DOI: https://doi.org/10.1021/acscatal.8b03151

Macromolecule Content

Total Structure Weight: 63.96 kDa
Atom Count: 5,064
Modeled Residue Count: 531
Deposited Residue Count: 532
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
molecule A	A, B	266	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0 Gene Names: DR_0132
UniProt
Find proteins for Q9RY20 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RY20 Go to UniProtKB: Q9RY20
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RY20
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain N [auth B] SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	C [auth A], E [auth A], L [auth B], N [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain L [auth B] Focus chain N [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B]	K [auth A], R [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain K [auth A] Focus chain R [auth B] Interactions & Density Focus chain K [auth A] Focus chain R [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A], J [auth A], P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain M [auth B] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain O [auth B] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain O [auth B] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A], F [auth A], M [auth B], O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.186 (Depositor), 0.187 (DCC)
R-Value Work: 0.162 (Depositor), 0.163 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.376	α = 90
b = 88.376	β = 90
c = 190.016	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-01-16

Deposition Author(s):

Nocek, B.

Joachimiak, A.

Yakunin, A.

Revision History (Full details and data files)

Version 1.0: 2019-01-16
Type: Initial release
Version 1.1: 2019-12-25
Changes: Database references
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description