5GR9
Crystal structure of PXY-TDIF/CLE41
- PDB DOI: https://doi.org/10.2210/pdb5GR9/pdb
- Classification: TRANSFERASE
- Organism(s): Arabidopsis thaliana, Arabidopsis
- Expression System: Spodoptera frugiperda
- Mutation(s): No 
- Deposited: 2016-08-08 Released: 2016-11-23 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.77 Å
- R-Value Free: 0.241 
- R-Value Work: 0.193 
- R-Value Observed: 0.195 
This is version 1.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Leucine-rich repeat receptor-like protein kinase TDR | A [auth B] | 599 | Arabidopsis thaliana | Mutation(s): 0  Gene Names: PXY EC: 2.7.11.1 | |
UniProt | |||||
Find proteins for Q9FII5 (Arabidopsis thaliana) Explore Q9FII5  Go to UniProtKB:  Q9FII5 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q9FII5 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
TDIF/CLE41 | B [auth C] | 12 | Arabidopsis | Mutation(s): 0  | |
UniProt | |||||
Find proteins for Q84W98 (Arabidopsis thaliana) Explore Q84W98  Go to UniProtKB:  Q84W98 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q84W98 | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | C [auth B] D [auth B] E [auth B] F [auth B] G [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
HYP Query on HYP | B [auth C] | L-PEPTIDE LINKING | C5 H9 N O3 | PRO |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.77 Å
- R-Value Free: 0.241 
- R-Value Work: 0.193 
- R-Value Observed: 0.195 
- Space Group: P 41 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 93.668 | α = 90 |
b = 93.668 | β = 90 |
c = 228.709 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2016-11-23  Deposition Author(s): Chai, J.J., Zhang, H.Q.
Revision History (Full details and data files)
- Version 1.0: 2016-11-23
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary