2JXR

STRUCTURE OF YEAST PROTEINASE A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.193 

wwPDB Validation   3D Report Full Report


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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEINASE A329Saccharomyces cerevisiaeMutation(s): 1 
EC: 3.4.23.25
UniProt
Find proteins for P07267 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07267 
Go to UniProtKB:  P07267
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07267
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86273CV
GlyCosmos:  G86273CV
GlyGen:  G86273CV
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2Z3
Query on 2Z3
Download Ideal Coordinates CCD File 
C [auth A]N-(morpholin-4-ylcarbonyl)-L-phenylalanyl-N-[(1R)-1-(cyclohexylmethyl)-3,3-difluoro-2,2-dihydroxy-4-(methylamino)-4-oxobutyl]-L-norleucinamide
C32 H49 F2 N5 O7
IPZOKQNUWWOCTK-GSDHBNRESA-N
NAG
Query on NAG
Download Ideal Coordinates CCD File 
D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2Z3 Binding MOAD:  2JXR Ki: 90 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChains NameType/Class2D Diagram3D Interactions
PRD_000416 (2Z3)
Query on PRD_000416		C [auth A]CP-81,282, MOR-PHE-NLE-CHF-NMEPeptide-like / Inhibitor
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.193 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.7α = 90
b = 86.7β = 90
c = 110.4γ = 120
Software Package:
Software NamePurpose
WEISdata collection
Agrovatadata reduction
RESTRAINrefinement
WEISdata reduction
Agrovatadata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-10-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
  • Version 2.1: 2021-11-03
    Changes: Database references, Structure summary