5MZV

IL-23:IL-23R:Nb22E11 complex

PDB DOI: https://doi.org/10.2210/pdb5MZV/pdb

Classification: CYTOKINE
Organism(s): Homo sapiens, Lama glama
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2017-02-01 Released: 2018-01-03
Deposition Author(s): Bloch, Y., Savvides, S.N.
Funding Organization(s): VLAIO

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.250
R-Value Work: 0.212
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 117.96 kDa
Atom Count: 7,116
Modelled Residue Count: 856
Deposited Residue Count: 1,012
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	328	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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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-23 subunit alpha	B	198	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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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-23 receptor	C	330	Homo sapiens	Mutation(s): 0 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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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 22E11	D	156	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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	E	7		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G07617FP GlyCosmos: G07617FP GlyGen: G07617FP

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, H, I	2		N-Glycosylation	Interactions Focus chain F Focus chain H Focus chain I Interactions & Density Focus chain F Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
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	G	3		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C]	N [auth C], O [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain N [auth C] Focus chain O [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain J [auth A] SDF format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain J [auth A] MOL2 format, chain M [auth C]	J [auth A], L [auth C], M [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain J [auth A] Focus chain L [auth C] Focus chain M [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.250
R-Value Work: 0.212
R-Value Observed: 0.214
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.219	α = 90
b = 112.19	β = 106.24
c = 109.87	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-01-03

Deposition Author(s):

Bloch, Y.

Savvides, S.N.

Funding Organization	Location	Grant Number
VLAIO	Belgium	--

Revision History (Full details and data files)

Version 1.0: 2018-01-03
Type: Initial release
Version 1.1: 2018-01-10
Changes: Database references
Version 1.2: 2018-01-31
Changes: Database references
Version 1.3: 2018-02-07
Changes: Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary