6WDQ

IL23/IL23R/IL12Rb1 signaling complex

PDB DOI: https://doi.org/10.2210/pdb6WDQ/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2020-04-01 Released: 2021-02-24
Deposition Author(s): Jude, K.M., Ely, L.K., Glassman, C.R., Thomas, C., Spangler, J.B., Lupardus, P.J., Garcia, K.C.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.295
R-Value Work: 0.238
R-Value Observed: 0.243

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 116.49 kDa
Atom Count: 6,845
Modelled Residue Count: 852
Deposited Residue Count: 1,005
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-12 subunit beta	A	308	Homo sapiens	Mutation(s): 0 Gene Names: IL12B, NKSF2
UniProt & NIH Common Fund Data Resources
Find proteins for P29460 (Homo sapiens) Explore P29460 Go to UniProtKB: P29460
PHAROS: P29460 GTEx: ENSG00000113302
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29460
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-23 subunit alpha	B	171	Homo sapiens	Mutation(s): 0 Gene Names: IL23A, SGRF, UNQ2498/PRO5798
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPF7 (Homo sapiens) Explore Q9NPF7 Go to UniProtKB: Q9NPF7
PHAROS: Q9NPF7 GTEx: ENSG00000110944
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NPF7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-23 receptor	C	307	Homo sapiens	Mutation(s): 1 Gene Names: IL23R
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VWK5 (Homo sapiens) Explore Q5VWK5 Go to UniProtKB: Q5VWK5
PHAROS: Q5VWK5 GTEx: ENSG00000162594
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5VWK5
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-12 receptor subunit beta-1	D	219	Homo sapiens	Mutation(s): 0 Gene Names: IL12RB1, IL12R, IL12RB
UniProt & NIH Common Fund Data Resources
Find proteins for P42701 (Homo sapiens) Explore P42701 Go to UniProtKB: P42701
PHAROS: P42701 GTEx: ENSG00000096996
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42701
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
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	E	3		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	2		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C]	G [auth A], H [auth C], I [auth C], J [auth C], K [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.295
R-Value Work: 0.238
R-Value Observed: 0.243
Space Group: P 2 2₁ 2₁
Diffraction Data: https://doi.org/10.15785/SBGRID/829

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.712	α = 90
b = 118.483	β = 90
c = 186.151	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-02-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)		5R01CA177684

Revision History (Full details and data files)

Version 1.0: 2021-02-24
Type: Initial release
Version 1.1: 2021-03-03
Changes: Database references
Version 1.2: 2021-05-05
Changes: Database references
Version 1.3: 2023-10-18
Changes: Data collection, Database references, Refinement description