5U3D

STRUCTURE OF MEDITOPE ENABLED TRASTUZUMAB I83E VARIANT

• PDB DOI: https://doi.org/10.2210/pdb5U3D/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Finegoldia magna, Staphylococcus aureus
• Expression System: Cricetulus griseus, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-12-01 Released: 2018-03-14 
• Deposition Author(s): Bzymek, K.P., Avery, K.N., Zer, C., Williams, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.185 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 

Literature

Meditope Enabled Trastuzumab I83E Variant

Bzymek, K.P., Avery, K.N., Zer, C., Williams, J.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60.45 kDa 
• Atom Count: 5,161 
• Modelled Residue Count: 552 
• Deposited Residue Count: 556 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MEMAB TRASTUZUMAB FAB LIGHT CHAIN I83E	A	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MEMAB TRASTUZUMAB FAB HEAVY CHAIN	B	223	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein L	C [auth E]	65	Finegoldia magna	Mutation(s): 5
UniProt
Find proteins for Q51918 (Finegoldia magna) Explore Q51918  Go to UniProtKB:  Q51918

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin G binding protein A	D [auth C]	54	Staphylococcus aureus	Mutation(s): 0  Gene Names: spa
UniProt
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P02976  Go to UniProtKB:  P02976

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRY	E [auth A]	MESO-ERYTHRITOL C4 H10 O4 UNXHWFMMPAWVPI-ZXZARUISSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.185 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.85	α = 90
b = 104.65	β = 90
c = 116.88	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): Bzymek, K.P., Avery, K.N., Zer, C., Williams, J.C.

Revision History  

• Version 1.0: 2018-03-14
  Type: Initial release
  
• Version 1.1: 2018-03-28
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2018-04-18
  Changes: Data collection
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description