3HC4 | pdb_00003hc4

BHA10 IgG1 Fab quadruple mutant variant - antibody directed at human LTBR

• PDB DOI: https://doi.org/10.2210/pdb3HC4/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2009-05-05 Released: 2009-08-04 
• Deposition Author(s): Arndt, J.W., Jordan, J.L., Lugovskoy, A., Wang, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.180 (Depositor) 
• R-Value Work: 
  0.161 (Depositor) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Structural understanding of stabilization patterns in engineered bispecific Ig-like antibody molecules

Jordan, J.L., Arndt, J.W., Hanf, K., Li, G., Hall, J., Demarest, S., Huang, F., Wu, X., Miller, B., Glaser, S., Fernandez, E.J., Wang, D., Lugovskoy, A.

(2009) Proteins 77: 832-841

• PubMed: 19626705 
• DOI: https://doi.org/10.1002/prot.22502
• Primary Citation Related Structures: 
  3HC0, 3HC3, 3HC4


• PubMed Abstract: 
  

  Bispecific immunoglobulin-like antibodies capable of engaging multiple antigens represent a promising new class of therapeutic agents. Engineering of these molecules requires optimization of the molecular properties of one of the domain components. Here, we present a detailed crystallographic and computational characterization of the stabilization patterns in the lymphotoxin-beta receptor (LTbetaR) binding Fv domain of an anti-LTbetaR/anti-TNF-related apoptosis inducing ligand receptor-2 (TRAIL-R2) bispecific immunoglobulin-like antibody. We further describe a new hierarchical structure-guided approach toward engineering of antibody-like molecules to enhance their thermal and chemical stability.

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Organizational Affiliation: 
• Biogen Idec, Inc., 12 Cambridge Center, Cambridge, Massachusetts 02142, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 46.57 kDa 
• Atom Count: 3,839 
• Modeled Residue Count: 425 
• Deposited Residue Count: 426 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN IGG1 FAB, HEAVY CHAIN	A [auth H]	213	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN IGG1 FAB, LIGHT CHAIN	B [auth L]	213	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth L], E [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	C [auth H], F [auth L], G [auth L]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.180 (Depositor) 
• R-Value Work:  0.161 (Depositor) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.605	α = 90
b = 118.233	β = 90
c = 126.452	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-04 
Deposition Author(s): Arndt, J.W., Jordan, J.L., Lugovskoy, A., Wang, D.

Revision History  

• Version 1.0: 2009-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-27
  Changes: Structure summary