2QFP

Crystal structure of red kidney bean purple acid phosphatase in complex with fluoride

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 


Literature

Crystal structures of a purple acid phosphatase, representing different steps of this enzyme's catalytic cycle.

Schenk, G., Elliott, T.W., Leung, E., Carrington, L.E., Mitic, N., Gahan, L.R., Guddat, L.W.

(2008) BMC Struct Biol 8: 6-6

  • DOI: https://doi.org/10.1186/1472-6807-8-6
  • Primary Citation of Related Structures:  
    2QFP, 2QFR

  • PubMed Abstract: 

    • Purple acid phosphatases belong to the family of binuclear metallohydrolases and are involved in a multitude of biological functions, ranging from bacterial killing and bone metabolism in animals to phosphate uptake in plants. Due to its role in bone resorption purple acid phosphatase has evolved into a promising target for the development of anti-osteoporotic chemotherapeutics ...

    Purple acid phosphatases belong to the family of binuclear metallohydrolases and are involved in a multitude of biological functions, ranging from bacterial killing and bone metabolism in animals to phosphate uptake in plants. Due to its role in bone resorption purple acid phosphatase has evolved into a promising target for the development of anti-osteoporotic chemotherapeutics. The design of specific and potent inhibitors for this enzyme is aided by detailed knowledge of its reaction mechanism. However, despite considerable effort in the last 10 years various aspects of the basic molecular mechanism of action are still not fully understood.

    Organizational Affiliation: 

    School of Molecular and Microbial Sciences, The University of Queensland, St, Lucia, QLD 4072, Australia. schenk@uq.edu.au



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purple acid phosphatase
A, B, C, D
424Phaseolus vulgarisMutation(s): 0 
EC: 3.1.3.2
UniProt
Find proteins for P80366 (Phaseolus vulgaris)
Explore P80366 
Go to UniProtKB:  P80366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80366
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
GA [auth C]
HA [auth C]
I [auth A]
IA [auth C]
J [auth A]
GA [auth C],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
L [auth A],
TA [auth D],
UA [auth D],
V [auth B],
VA [auth D],
W [auth B],
WA [auth D],
X [auth B],
Y [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
SO4
Query on SO4
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EA [auth C]
G [auth A]
NA [auth C]
OA [auth D]
P [auth A]
EA [auth C],
G [auth A],
NA [auth C],
OA [auth D],
P [auth A],
Q [auth B],
RA [auth D],
T [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
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DA [auth C],
F [auth A],
QA [auth D],
S [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
FE
Query on FE
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CA [auth C],
E [auth A],
PA [auth D],
R [auth B]		FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
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AA [auth B]
BA [auth B]
KA [auth C]
LA [auth C]
M [auth A]
AA [auth B],
BA [auth B],
KA [auth C],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
O [auth A],
XA [auth D],
YA [auth D],
Z [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
F
Query on F
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FA [auth C],
H [auth A],
SA [auth D],
U [auth B]		FLUORIDE ION
F
KRHYYFGTRYWZRS-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.719α = 90
b = 188.466β = 90
c = 192.398γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
EPMRphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary