7PLJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PPK2 domain-containing protein
A, B, C, D
266Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RY20
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

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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
ADP (Subject of Investigation/LOI)
Query on ADP

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DA [auth D],
G [auth A]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
7TT (Subject of Investigation/LOI)
Query on 7TT

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I [auth A]Tetraphosphate
H6 O13 P4
YDHWWBZFRZWVHO-UHFFFAOYSA-N
3PO (Subject of Investigation/LOI)
Query on 3PO

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H [auth A]TRIPHOSPHATE
H5 O10 P3
UNXRWKVEANCORM-UHFFFAOYSA-N
PPV (Subject of Investigation/LOI)
Query on PPV

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P [auth B],
U [auth C],
V [auth C]
PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
PEG
Query on PEG

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EA [auth D],
GA [auth D],
O [auth B],
W [auth C],
Y [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

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HA [auth D]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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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
MG (Subject of Investigation/LOI)
Query on MG

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IA [auth D],
K [auth A],
R [auth B],
Z [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.851α = 90
b = 137.144β = 116.895
c = 85.024γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugalPTDC/BIA-BQM/31317/2017

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description