5D63

MOA-Z-VAD-fmk inhibitor complex, direct/inverted dual orientation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 2.1 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 of 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.


Macromolecules
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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

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Z-VAD-fmkB [auth L]5synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D 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 Glycosylation3D 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 
I [auth A],
J [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

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N [auth A],
O [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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K [auth A],
L [auth A],
M [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
P [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.066α = 90
b = 121.066β = 90
c = 99.95γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
Cootmodel building
XDSdata scaling

Structure Validation

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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: Advisory, 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