3N2Z

The Structure of Human Prolylcarboxypeptidase at 2.80 Angstroms Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structural definition and substrate specificity of the S28 protease family: the crystal structure of human prolylcarboxypeptidase.

Soisson, S.M.Patel, S.B.Abeywickrema, P.D.Bryne, N.J.Diehl, R.E.Hall, D.L.Ford, R.E.Reid, J.C.Rickert, K.W.Shipman, J.M.Sharma, S.Lumb, K.J.

(2010) BMC Struct Biol 10: 16-16

  • DOI: https://doi.org/10.1186/1472-6807-10-16
  • Primary Citation of Related Structures:  
    3N2Z

  • PubMed Abstract: 

    The unique S28 family of proteases is comprised of the carboxypeptidase PRCP and the aminopeptidase DPP7. The structural basis of the different substrate specificities of the two enzymes is not understood nor has the structure of the S28 fold been described.


  • Organizational Affiliation

    Global Structural Biology, Merck Research Laboratories, P,O, Box 4, West Point, PA 19486, USA. stephen_soisson@merck.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysosomal Pro-X carboxypeptidaseA [auth B]446Homo sapiensMutation(s): 0 
Gene Names: PRCPPCP
EC: 3.4.16.2
UniProt & NIH Common Fund Data Resources
Find proteins for P42785 (Homo sapiens)
Explore P42785 
Go to UniProtKB:  P42785
PHAROS:  P42785
GTEx:  ENSG00000137509 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42785
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth A]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.14α = 90
b = 181.14β = 90
c = 240.13γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
TNTrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary