9MFG | pdb_00009mfg

Complex of IL23 receptor and VHH

PDB DOI: https://doi.org/10.2210/pdb9MFG/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Lama glama
Expression System: Trichoplusia ni, Cricetulus griseus
Mutation(s): No

Deposited: 2024-12-09 Released: 2025-05-21
Deposition Author(s): Kiefer, J.R., Wallweber, H.A., Koerber, J.T., Ota, N., Davies, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 ?
R-Value Free:
0.246 (Depositor), 0.246 (DCC)
R-Value Work:
0.204 (Depositor), 0.204 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Oral single domain antibody inhibition of IL-23 signaling

Ota, N., Davies, C., Wallweber, H.A., Kiefer, J.R., Koerber, J.T.

To be published.

Macromolecule Content

Total Structure Weight: 202.84 kDa
Atom Count: 13,510
Modeled Residue Count: 1,648
Deposited Residue Count: 1,696
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-23 receptor	A, B, C, D	304	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
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: Q5VWK5-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH	E, F, G, H	120	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: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I, T	3		N-Glycosylation	Interactions Focus chain I Focus chain T Interactions & Density Focus chain I Focus chain T

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, N, Q, R, U	2		N-Glycosylation	Interactions Focus chain J Focus chain N Focus chain Q Focus chain R Focus chain U Interactions & Density Focus chain J Focus chain N Focus chain Q Focus chain R Focus chain U

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	K, O	4		N-Glycosylation	Interactions Focus chain K Focus chain O Interactions & Density Focus chain K Focus chain O

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	L, P, S	4		N-Glycosylation	Interactions Focus chain L Focus chain P Focus chain S Interactions & Density Focus chain L Focus chain P Focus chain S

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	M	3		N-Glycosylation	Interactions Focus chain M Interactions & Density Focus chain M

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth C]	AA [auth D], V [auth A], W [auth A], Y [auth B], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain V [auth A] Focus chain W [auth A] Focus chain Y [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth D] Focus chain V [auth A] Focus chain W [auth A] Focus chain Y [auth B] Focus chain Z [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain GA [auth F] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth F] mmCIF format, chain FA [auth E] mmCIF format, chain GA [auth F]	FA [auth E], GA [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain FA [auth E] Focus chain GA [auth F] Interactions & Density Focus chain FA [auth E] Focus chain GA [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain EA [auth E] MOL2 format, chain EA [auth E] mmCIF format, chain EA [auth E]	EA [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Interactions & Density Focus chain EA [auth E]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain HA [auth G] SDF format, chain X [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain HA [auth G] MOL2 format, chain X [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain HA [auth G] mmCIF format, chain X [auth A]	BA [auth D], CA [auth D], DA [auth D], HA [auth G], X [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain HA [auth G] Focus chain X [auth A] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain HA [auth G] Focus chain X [auth A]