6AZT

Asparaginyl endopeptidase 1 bound to AAN peptide, a tetrahedral intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural basis of ribosomal peptide macrocyclization in plants.

Haywood, J.Schmidberger, J.W.James, A.M.Nonis, S.G.Sukhoverkov, K.V.Elias, M.Bond, C.S.Mylne, J.S.

(2018) Elife 7: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Asparaginyl endopeptidase 1
A
491Helianthus annuusGene Names: VPE
Find proteins for A0A251RPF5 (Helianthus annuus)
Go to UniProtKB:  A0A251RPF5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ASN tetrahedral intermediate
B
3N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SNN
Query on SNN
A
L-PEPTIDE LINKINGC4 H6 N2 O2ASN
CE7
Query on CE7
B
L-peptide linkingC4 H10 N2 O4ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.152 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 77.030α = 90.00
b = 77.030β = 90.00
c = 108.171γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
Aimlessdata scaling
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-09-13 
  • Released Date: 2018-02-07 
  • Deposition Author(s): Bond, C.S.

Funding OrganizationCountryGrant Number
Australian Research CouncilAustraliaDP160100107

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 2.0: 2018-05-16
    Type: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Structure summary