1EK3 | pdb_00001ek3

KAPPA-4 IMMUNOGLOBULIN VL, REC

• PDB DOI: https://doi.org/10.2210/pdb1EK3/pdb

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


• Deposited: 2000-03-06 Released: 2001-03-06 
• Deposition Author(s): Pokkuluri, P.R., Huang, D.-B., Raffen, R., Stevens, F.J., Schiffer, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

The Structure of Amyloidogenic Kappa-4 Immunoglobulin VL, REC

Pokkuluri, P.R., Huang, D.-B., Raffen, R., Stevens, F.J., Schiffer, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 25.01 kDa 
• Atom Count: 2,018 
• Modeled Residue Count: 228 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KAPPA-4 IMMUNOGLOBULIN LIGHT CHAIN VL	A, B	114	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P06312 (Homo sapiens) Explore P06312  Go to UniProtKB:  P06312
PHAROS:  P06312 GTEx:  ENSG00000211598

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.58	α = 90
b = 66.91	β = 90
c = 91.5	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-03-06 
Deposition Author(s): Pokkuluri, P.R., Huang, D.-B., Raffen, R., Stevens, F.J., Schiffer, M.

Revision History  

• Version 1.0: 2001-03-06
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-09
  Changes: Structure summary