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


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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysosomal Pro-X carboxypeptidaseA [auth B]446Homo sapiensMutation(s): 0 
Gene Names: PRCPPCP
EC: 3.4.16.2
Find proteins for P42785 (Homo sapiens)
Explore P42785 
Go to UniProtKB:  P42785
NIH Common Fund Data Resources
PHAROS:  P42785
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth A]2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth B], D [auth B], E [auth B], F [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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



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