3N85

Crystallographic trimer of HER2 extracellular regions in complex with tryptophan-rich antibody fragment

• PDB DOI: https://doi.org/10.2210/pdb3N85/pdb

• Classification: Transferase/immune system
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-27 Released: 2010-07-28 
• Deposition Author(s): Eigenbrot, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.230 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 

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

Macromolecule Content

• Total Structure Weight: 119.43 kDa 
• Atom Count: 8,114 
• Modelled Residue Count: 1,033 
• Deposited Residue Count: 1,065 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-2	A	624	Homo sapiens	Mutation(s): 0  Gene Names: ERBB2, HER2, MLN19, NEU, NGL EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04626 (Homo sapiens) Explore P04626  Go to UniProtKB:  P04626
PHAROS:  P04626 GTEx:  ENSG00000141736

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab37 Light Chain	B [auth L]	217	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab37 Heavy Chain	C [auth H]	224	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

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 [auth C]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth L], U [auth L], V [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.230 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.22	α = 90
b = 182.22	β = 90
c = 330.851	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Eigenbrot, C.

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-01-15
  Changes: Refinement description
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary