5C2B | pdb_00005c2b

anti-CXCL13 parental scFv - 3B4

• PDB DOI: https://doi.org/10.2210/pdb5C2B/pdb

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


• Deposited: 2015-06-15 Released: 2015-11-04 
• Deposition Author(s): Tu, C., Bard, J., Mosyak, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.194 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Optimization of a scFv-based biotherapeutic by CDR side-chain clash repair

Tu, C., Terrabube, V., Tam, A., Stochaj, W., Fennell, B., Lin, L., Stahl, M., LaVallie, E., Somers, W., Finlay, W., Mosyak, L., Bard, J., Cunningham, O.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.67 kDa 
• Atom Count: 2,268 
• Modeled Residue Count: 241 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv 3B4	A [auth H]	254	Homo sapiens	Mutation(s): 0  Gene Names: IGHV1-69D, IGHV1-69-2
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J2H0 (Homo sapiens) Explore A0A0B4J2H0  Go to UniProtKB:  A0A0B4J2H0
GTEx:  ENSG00000280411
Find proteins for A0A5C2GBJ8 (Homo sapiens) Explore A0A5C2GBJ8  Go to UniProtKB:  A0A5C2GBJ8
UniProt Groups	A0A5C2GBJ8A0A0B4J2H0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth H], C [auth H], D [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.194 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.9	α = 90
b = 133.5	β = 90
c = 44.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-04 
Deposition Author(s): Tu, C., Bard, J., Mosyak, L.

Revision History  

• Version 1.0: 2015-11-04
  Type: Initial release
  
• Version 1.1: 2017-11-01
  Changes: Author supporting evidence, Derived calculations
• Version 2.0: 2019-12-25
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.0: 2020-06-17
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 3.1: 2024-10-30
  Changes: Data collection, Database references, Refinement description, Structure summary