5D61 | pdb_00005d61

MOA-Z-VAD-fmk complex, direct orientation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.186 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history

Literature

An Unusual Member of the Papain Superfamily: Mapping the Catalytic Cleft of the Marasmius oreades agglutinin (MOA) with a Caspase Inhibitor.

Cordara, G.van Eerde, A.Grahn, E.M.Winter, H.C.Goldstein, I.J.Krengel, U.

(2016) PLoS One 11: e0149407-e0149407

  • DOI: https://doi.org/10.1371/journal.pone.0149407
  • Primary Citation Related Structures: 
    5D61, 5D62, 5D63

  • PubMed Abstract: 

    Papain-like cysteine proteases (PLCPs) constitute the largest group of thiol-based protein degrading enzymes and are characterized by a highly conserved fold. They are found in bacteria, viruses, plants and animals and involved in a number of physiological and pathological processes, parasitic infections and host defense, making them interesting targets for drug design. The Marasmius oreades agglutinin (MOA) is a blood group B-specific fungal chimerolectin with calcium-dependent proteolytic activity. The proteolytic domain of MOA presents a unique structural arrangement, yet mimicking the main structural elements in known PLCPs. Here we present the X-ray crystal structure of MOA in complex with Z-VAD-fmk, an irreversible caspase inhibitor known to cross-react with PLCPs. The structural data allow modeling of the substrate binding geometry and mapping of the fundamental enzyme-substrate interactions. The new information consolidates MOA as a new, yet strongly atypical member of the papain superfamily. The reported complex is the first published structure of a PLCP in complex with the well characterized caspase inhibitor Z-VAD-fmk.


  • Organizational Affiliation
    • Department of Chemistry, University of Oslo, Oslo, Norway.

Macromolecule Content 

  • Total Structure Weight: 34.67 kDa 
  • Atom Count: 2,753 
  • Modeled Residue Count: 297 
  • Deposited Residue Count: 298 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Agglutinin293Marasmius oreadesMutation(s): 0 
UniProt
Find proteins for Q8X123 (Marasmius oreades)
Explore Q8X123 
Go to UniProtKB:  Q8X123
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8X123
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Z-VAD-fmkB [auth L]5synthetic constructMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranoseC [auth B]3N/A
Glycosylation Resources
GlyTouCan: G47548GA
GlyCosmos: G47548GA
GlyGen: G47548GA
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranoseD [auth C],
E [auth D]
3N/A
Glycosylation Resources
GlyTouCan: G11065GA
GlyCosmos: G11065GA
GlyGen: G11065GA

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DMS

Query on DMS



Download:Ideal Coordinates CCD File
L [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
M [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.607α = 90
b = 120.607β = 90
c = 100.129γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
Cootmodel building
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Non-polymer description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-10-23
    Changes: Structure summary