5U6A | pdb_00005u6a

CRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO-PEG3-MEDITOPE

• PDB DOI: https://doi.org/10.2210/pdb5U6A/pdb

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


• Deposited: 2016-12-07 Released: 2018-03-14 
• Deposition Author(s): Williams, J.C., Bzymek, K.P., Pucket, J., Avery, K.A., Ma, Y., Xie, J., Zer, C., Horne, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.188 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Of I83E Meditope-Enabled Trastuzumab With Azido-PEG3-Meditope

Williams, J.C., Bzymek, K.P., Pucket, J., Avery, K.A., Ma, Y., Xie, J., Zer, C., Horne, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 62.15 kDa 
• Atom Count: 5,469 
• Modeled Residue Count: 568 
• Deposited Residue Count: 568 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain	A	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain	B	223	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein L	C [auth E]	63	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

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
meditope peptide	E [auth D]	14	synthetic construct	Mutation(s): 0

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2GX	E [auth D]	L-PEPTIDE LINKING	C15 H15 N O2		PHE
562	E [auth D]	L-PEPTIDE LINKING	C12 H26 N7 O4		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.188 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.25	α = 90
b = 105.17	β = 90
c = 117.07	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-14 
Deposition Author(s): Williams, J.C., Bzymek, K.P., Pucket, J., Avery, K.A., Ma, Y., Xie, J., Zer, C., Horne, D.

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
• Version 1.4: 2023-11-15
  Changes: Data collection, Derived calculations