4LEO

Crystal structure of anti-HER3 Fab RG7116 in complex with the extracellular domains of human Her3 (ERBB3)

• PDB DOI: https://doi.org/10.2210/pdb4LEO/pdb

• Classification: Transferase/Immune System
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2013-06-26 Released: 2013-07-10 
• Deposition Author(s): Schiller, C.B., Hopfner, K.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.258 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 118.51 kDa 
• Atom Count: 8,185 
• Modelled Residue Count: 1,034 
• Deposited Residue Count: 1,068 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RG7116 Fab heavy chain	A	227	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RG7116 Fab light chain	B	220	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-3	C	621	Homo sapiens	Mutation(s): 0  Gene Names: ERBB3, HER3 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P21860 (Homo sapiens) Explore P21860  Go to UniProtKB:  P21860
PHAROS:  P21860 GTEx:  ENSG00000065361

Oligosaccharides

Help

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	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth C], F [auth C], G [auth C], H [auth C], I [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.258 
• R-Value Work: 0.228 
• R-Value Observed: 0.230 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.458	α = 97.64
b = 59.359	β = 106.85
c = 103.661	γ = 96.83

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-10 
Deposition Author(s): Schiller, C.B., Hopfner, K.P.

Revision History  

• Version 1.0: 2013-07-10
  Type: Initial release
  
• Version 1.1: 2013-08-28
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Advisory, Refinement description
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary