5J2S | pdb_00005j2s

NKR-P1B from Rattus norvegicus

• PDB DOI: https://doi.org/10.2210/pdb5J2S/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-03-30 Released: 2017-10-11 
• Deposition Author(s): Skalova, T., Vanek, O., Blaha, J., Duskova, J., Hasek, J., Koval, T., Dohnalek, J.
• Funding Organization(s): Czech Science Foundation, European Regional Development Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.262 (Depositor) 
• R-Value Work: 
  0.221 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Structure of NKR-P1B from Rattus norvegicus

Vanek, O., Skalova, T., Blaha, J., Duskova, J., Hasek, J., Koval, T., Dohnalek, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 34.66 kDa 
• Atom Count: 2,121 
• Modeled Residue Count: 244 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Killer cell lectin-like receptor subfamily B member 1B allele A	A, B	149	Rattus norvegicus	Mutation(s): 0  Gene Names: Klrb1b, Nkrp1b
UniProt
Find proteins for A4KWA1 (Rattus norvegicus) Explore A4KWA1  Go to UniProtKB:  A4KWA1
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: A4KWA1-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.262 (Depositor) 
• R-Value Work:  0.221 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.721	α = 90
b = 60.721	β = 90
c = 76.589	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Skalova, T., Vanek, O., Blaha, J., Duskova, J., Hasek, J., Koval, T., Dohnalek, J.

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Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	15-15181S
European Regional Development Fund	Czech Republic	CZ.1.05/1.1.00/02.0109

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 2.0: 2019-04-24
  Changes: Data collection, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary