3MZW

HER2 extracelluar region with affinity matured 3-helix affibody ZHER2:342

• PDB DOI: https://doi.org/10.2210/pdb3MZW/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, Staphylococcus aureus
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2010-05-13 Released: 2010-07-28 
• Deposition Author(s): Eigenbrot, C., Ultsch, M.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.278 
• R-Value Work: 0.204 
• R-Value Observed: 0.208 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.38 kDa 
• Atom Count: 4,890 
• Modelled Residue Count: 622 
• Deposited Residue Count: 682 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine kinase-type cell surface receptor HER2	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
Immunoglobulin G-binding protein A	B	58	Staphylococcus aureus	Mutation(s): 14
UniProt
Find proteins for P38507 (Staphylococcus aureus) Explore P38507  Go to UniProtKB:  P38507

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	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	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.278 
• R-Value Work: 0.204 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.726	α = 90
b = 97.841	β = 90
c = 148.283	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

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