5YSP

Pyrophosphate-dependent kinase in the ribokinase family complexed with a pyrophosphate analog and myo-inositol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants.

Nagata, R.Fujihashi, M.Sato, T.Atomi, H.Miki, K.

(2018) Nat Commun 9: 1765-1765


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TM0415
A, B
286Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Find proteins for Q9WYP6 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9WYP6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MDN
Query on MDN

Download SDF File 
Download CCD File 
A
METHYLENEDIPHOSPHONIC ACID
C H6 O6 P2
MBKDYNNUVRNNRF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
INS
Query on INS

Download SDF File 
Download CCD File 
A, B
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
MYO-INOSITOL
C6 H12 O6
CDAISMWEOUEBRE-GPIVLXJGSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.673α = 90.00
b = 63.009β = 105.05
c = 89.884γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
Cootmodel building
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan16J08482
Japan Society for the Promotion of ScienceJapan17H05439

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release