4YH7

Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1

• PDB DOI: https://doi.org/10.2210/pdb4YH7/pdb

• Classification: HYDROLASE/IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2015-02-27 Released: 2015-05-06 
• Deposition Author(s): Yamagata, A., Fukai, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.40 Å
• R-Value Free: 0.325 
• R-Value Work: 0.290 
• R-Value Observed: 0.292 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 135.15 kDa 
• Atom Count: 7,240 
• Modelled Residue Count: 909 
• Deposited Residue Count: 1,189 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-type tyrosine-protein phosphatase delta	A	841	Mus musculus	Mutation(s): 0  Gene Names: Ptprd EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q64487 (Mus musculus) Explore Q64487  Go to UniProtKB:  Q64487
IMPC:  MGI:97812

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 receptor accessory protein-like 1	B	348	Mus musculus	Mutation(s): 0  Gene Names: Il1rapl1
UniProt
Find proteins for P59823 (Mus musculus) Explore P59823  Go to UniProtKB:  P59823

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	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth B], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.40 Å
• R-Value Free: 0.325 
• R-Value Work: 0.290 
• R-Value Observed: 0.292 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 286.295	α = 90
b = 286.295	β = 90
c = 70.183	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-06 
Deposition Author(s): Yamagata, A., Fukai, S.

Revision History  

• Version 1.0: 2015-05-06
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Derived calculations, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Experimental preparation, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary