6WGL

Dupilumab fab with Crystal Kappa design complexed with human IL-4 receptor

PDB DOI: https://doi.org/10.2210/pdb6WGL/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2020-04-05 Released: 2020-09-16
Deposition Author(s): Druzina, Z., Atwell, S., Pustilnik, A., Antonysamy, S., Ho, C., Lieu, R., Hendle, J., Benach, J., Wang, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free: 0.304
R-Value Work: 0.245
R-Value Observed: 0.248

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: 75.02 kDa
Atom Count: 4,743
Modelled Residue Count: 616
Deposited Residue Count: 669
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dupilumab Fab heavy chain	A	234	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dupilumab Fab light chain	B	217	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-4 receptor subunit alpha	C	218	Homo sapiens	Mutation(s): 0 Gene Names: IL4R, IL4RA, 582J2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P24394 (Homo sapiens) Explore P24394 Go to UniProtKB: P24394
PHAROS: P24394 GTEx: ENSG00000077238
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24394
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	D, E	2		N-Glycosylation	Interactions Focus chain D Focus chain E Interactions & Density Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C]	F [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free: 0.304
R-Value Work: 0.245
R-Value Observed: 0.248
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.49	α = 90
b = 73.49	β = 90
c = 412.441	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-09-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-09-16
Type: Initial release
Version 2.0: 2020-09-23
Changes: Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2023-10-18
Changes: Data collection, Database references, Refinement description