7PLJ | pdb_00007plj

Structure of Polyphosphate kinase 2 from Deinococcus radiodurans, in complex with ATP and polyphosphates.

PDB DOI: https://doi.org/10.2210/pdb7PLJ/pdb

Classification: TRANSFERASE
Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-08-31 Released: 2023-03-22
Deposition Author(s): Silva, S.T.N., Romao, C.V.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.202 (Depositor), 0.198 (DCC)
R-Value Work:
0.169 (Depositor), 0.166 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of Polyphosphate kinase 2 from Deinococcus radiodurans, in complex with ATP and polyphosphates.

Silva, S.T.N., Romao, C.V.

To be published.

Macromolecule Content

Total Structure Weight: 129.51 kDa
Atom Count: 10,455
Modeled Residue Count: 1,064
Deposited Residue Count: 1,064
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PPK2 domain-containing protein	A, B, C, D	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 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain L [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	AA [auth D] BA [auth D] E [auth A] F [auth A] L [auth B] AA [auth D], BA [auth D], E [auth A], F [auth A], L [auth B], M [auth B], S [auth C], T [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain T [auth C]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain G [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain G [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain G [auth A]	DA [auth D], G [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain DA [auth D] Focus chain G [auth A] Interactions & Density Focus chain DA [auth D] Focus chain G [auth A]
7TT (Subject of Investigation/LOI) Query on 7TT Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	Tetraphosphate H₆ O₁₃ P₄ YDHWWBZFRZWVHO-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
3PO (Subject of Investigation/LOI) Query on 3PO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	TRIPHOSPHATE H₅ O₁₀ P₃ UNXRWKVEANCORM-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
PPV (Subject of Investigation/LOI) Query on PPV Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain V [auth C] SDF format, chain U [auth C] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] mmCIF format, chain P [auth B] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C]	P [auth B], U [auth C], V [auth C]	PYROPHOSPHATE H₄ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain GA [auth D] SDF format, chain O [auth B] SDF format, chain W [auth C] SDF format, chain Y [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain W [auth C] mmCIF format, chain Y [auth C]	EA [auth D], GA [auth D], O [auth B], W [auth C], Y [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain GA [auth D] Focus chain O [auth B] Focus chain W [auth C] Focus chain Y [auth C] Interactions & Density Focus chain EA [auth D] Focus chain GA [auth D] Focus chain O [auth B] Focus chain W [auth C] Focus chain Y [auth C]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain HA [auth D] MOL2 format, chain HA [auth D] mmCIF format, chain HA [auth D]	HA [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain HA [auth D] Interactions & Density Focus chain HA [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain X [auth C] SDF format, chain Q [auth B] SDF format, chain CA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain CA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain X [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain CA [auth D]	CA [auth D] FA [auth D] J [auth A] N [auth B] Q [auth B] CA [auth D], FA [auth D], J [auth A], N [auth B], Q [auth B], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain FA [auth D] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth B] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain FA [auth D] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth B] Focus chain X [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain Z [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Z [auth C]	IA [auth D], K [auth A], R [auth B], Z [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain IA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain Z [auth C] Interactions & Density Focus chain IA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain Z [auth C]