2X4D | pdb_00002x4d

Crystal structure of human phospholysine phosphohistidine inorganic pyrophosphate phosphatase LHPP

• PDB DOI: https://doi.org/10.2210/pdb2X4D/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-01-29 Released: 2010-03-16 
• Deposition Author(s): 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.

---

Experimental Data Snapshot

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

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.14 kDa 
• Atom Count: 3,704 
• Modeled Residue Count: 483 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOLYSINE PHOSPHOHISTIDINE INORGANIC PYROPHOSPHATE PHOSPHATASE	A, B	271	Homo sapiens	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	E [auth A], I [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
POP	C [auth A], G [auth B]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	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 (Depositor) 
• R-Value Work:  0.227 (Depositor) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.21	α = 90
b = 39.41	β = 91.79
c = 112.92	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-16 
Deposition Author(s): 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.

Revision History  

• 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