4NZD

Interleukin 21 receptor

PDB DOI: https://doi.org/10.2210/pdb4NZD/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2013-12-12 Released: 2014-12-17
Deposition Author(s): Hamming, O.T., Kang, L., Siupka, P., Gad, H.H., Hartmann, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.275
R-Value Work: 0.239
R-Value Observed: 0.241

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 80.6 kDa
Atom Count: 5,498
Modelled Residue Count: 628
Deposited Residue Count: 657
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-21 receptor	A, B, C	219	Homo sapiens	Mutation(s): 0 Gene Names: IL21R, NILR, UNQ3121/PRO10273
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HBE5 (Homo sapiens) Explore Q9HBE5 Go to UniProtKB: Q9HBE5
PHAROS: Q9HBE5 GTEx: ENSG00000103522
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HBE5
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F	5		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G00395TQ GlyCosmos: G00395TQ GlyGen: G00395TQ

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain X [auth C] SDF format, chain G [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth C] MOL2 format, chain G [auth A]	G [auth A], Q [auth B], X [auth C]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain G [auth A] Focus chain Q [auth B] Focus chain X [auth C] Interactions & Density Focus chain G [auth A] Focus chain Q [auth B] Focus chain X [auth C]
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain W [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain W [auth B]	O [auth A], P [auth A], W [auth B]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain W [auth B] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain W [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth C] MOL2 format, chain CA [auth C]	CA [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Interactions & Density Focus chain CA [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain M [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B]	AA [auth C] BA [auth C] K [auth A] L [auth A] M [auth A] AA [auth C], BA [auth C], K [auth A], L [auth A], M [auth A], N [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	H [auth A], I [auth A], J [auth A], Y [auth C], Z [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Y [auth C] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.275
R-Value Work: 0.239
R-Value Observed: 0.241
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.33	α = 90
b = 125.26	β = 90
c = 178.27	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
SOLVE	phasing
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-12-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-12-17
Type: Initial release
Version 1.1: 2018-03-07
Changes: Advisory, Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary