5GR8

Crystal structure of PEPR1-AtPEP1

• PDB DOI: https://doi.org/10.2210/pdb5GR8/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-08-08 Released: 2016-12-14 
• Deposition Author(s): Chai, J.J., Tang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.288 
• R-Value Work: 0.234 
• R-Value Observed: 0.237 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 160.44 kDa 
• Atom Count: 11,318 
• Modelled Residue Count: 1,453 
• Deposited Residue Count: 1,454 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat receptor-like protein kinase PEPR1	A, B [auth D]	710	Arabidopsis thaliana	Mutation(s): 0  Gene Names: PEPR1 EC: 2.7.11.1
UniProt
Find proteins for Q9SSL9 (Arabidopsis thaliana) Explore Q9SSL9  Go to UniProtKB:  Q9SSL9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elicitor peptide 1	C [auth J], D [auth P]	17	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9LV87 (Arabidopsis thaliana) Explore Q9LV87  Go to UniProtKB:  Q9LV87

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth B], F [auth C], G [auth E]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth A], I [auth A], J [auth A], K [auth A], M [auth D], N [auth D], O [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.288 
• R-Value Work: 0.234 
• R-Value Observed: 0.237 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.49	α = 90
b = 96.967	β = 110.79
c = 106.013	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Chai, J.J., Tang, J.

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary