4KUZ | pdb_00004kuz

Crystal structure of anti-emmprin antibody 4A5 Fab in trigonal form

• PDB DOI: https://doi.org/10.2210/pdb4KUZ/pdb

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


• Deposited: 2013-05-22 Released: 2014-03-26 
• Deposition Author(s): Teplyakov, A., Obmolova, G., Gilliland, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Models: experimental

Literature

Structural evidence for a constrained conformation of short CDR-L3 in antibodies.

Teplyakov, A., Obmolova, G., Malia, T.J., Luo, J., Gilliland, G.L.

(2014) Proteins 82: 1679-1683

• PubMed: 24470236 
• DOI: https://doi.org/10.1002/prot.24522
• Primary Citation of Related Structures:  
  4KQ3, 4KUZ


• PubMed Abstract: 
  

  Three Fab structures used as targets in the Antibody Modeling Assessment presented a challenge for modeling CDR-L3 due to deviations from the most typical canonical structure. In all three antibodies CDR-L3 has eight residues, which is one residue shorter than usual, and has a conformation that is rarely observed in crystal structures. We analyzed the sequence and structural determinants of this conformation and found that the "short" CDR-L3 is remarkably rigid and retains the conformation in the interactions with antigens and neighboring CDRs.

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Organizational Affiliation: 

Janssen Research & Development, LLC, Spring House, Pennsylvania, 19477.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 49.08 kDa 
• Atom Count: 3,402 
• Modelled Residue Count: 436 
• Deposited Residue Count: 448 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody 4A5 light chain	A [auth L]	219	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody 4A5 heavy chain	B [auth H]	229	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth L], D [auth L], E [auth H], F [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.43	α = 90
b = 126.43	β = 90
c = 97.15	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling
CrystalClear	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-26 
Deposition Author(s): Teplyakov, A., Obmolova, G., Gilliland, G.L.

Revision History  

• Version 1.0: 2014-03-26
  Type: Initial release
  
• Version 1.1: 2014-08-06
  Changes: Database references
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary