2X4D

Crystal structure of human phospholysine phosphohistidine inorganic pyrophosphate phosphatase LHPP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal Structure of Human Phospholysine Phosphohistidine Inorganic Pyrophosphate Phosphatase Lhpp

Vollmar, M., Gileadi, C., Guo, K., Savitsky, P., Muniz, J.R.C., Yue, W., Allerston, C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Kavanagh, K.L., Oppermann, U.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHOLYSINE PHOSPHOHISTIDINE INORGANIC PYROPHOSPHATE PHOSPHATASE
A, B
271Homo sapiensMutation(s): 2 
EC: 3.6.1.1 (PDB Primary Data), 3.1.3 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H008 (Homo sapiens)
Explore Q9H008 
Go to UniProtKB:  Q9H008
PHAROS:  Q9H008
GTEx:  ENSG00000107902 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H008
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE
Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]		4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
POP
Query on POP
Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]		PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
GOL
Query on GOL
Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.21α = 90
b = 39.41β = 91.79
c = 112.92γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Advisory, Database references, Structure summary
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description