1RPT

CRYSTAL STRUCTURES OF RAT ACID PHOSPHATASE COMPLEXED WITH THE TRANSITIONS STATE ANALOGS VANADATE AND MOLYBDATE: IMPLICATIONS FOR THE REACTION MECHANISM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structures of rat acid phosphatase complexed with the transition-state analogs vanadate and molybdate. Implications for the reaction mechanism.

Lindqvist, Y.Schneider, G.Vihko, P.

(1994) Eur J Biochem 221: 139-142

  • DOI: https://doi.org/10.1111/j.1432-1033.1994.tb18722.x
  • Primary Citation of Related Structures:  
    1RPT

  • PubMed Abstract: 

    The three-dimensional structures of complexes of recombinant rat prostatic acid phosphatase with the transition-state analogs vanadate and molybdate were determined to 0.3-nm resolution using protein crystallographic methods. The overall structure of the enzyme remains unchanged upon binding of the metal oxyanions; only local conformational differences in the positions of some side chains at the active site were found. The metal oxyanions bind in an identical fashion at the active site with trigonal bipyramidal coordination geometry. The metal ion is within coordination distance of the His12 side chain which is located at one of the axial positions. The three equatorial oxygen atoms interact with the conserved residues Arg11, Arg15, Arg79 and His257. Within hydrogen-bonding distance of the axial oxygen atom is the side chain of the conserved residue Asp258. The implications of these results for the catalytic mechanism of acid phosphatase are discussed.


  • Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROSTATIC ACID PHOSPHATASE342Rattus norvegicusMutation(s): 0 
EC: 3.1.3.2
UniProt
Find proteins for P20646 (Rattus norvegicus)
Explore P20646 
Go to UniProtKB:  P20646
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20646
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
VO4
Query on VO4

Download Ideal Coordinates CCD File 
D [auth A]VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.4α = 90
b = 89.4β = 90
c = 152γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-05-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Structure summary