4J4L

Modular evolution and design of the protein binding interface

• PDB DOI: https://doi.org/10.2210/pdb4J4L/pdb

• Classification: PROTEIN BINDING/CYTOKINE
• Organism(s): Listeria monocytogenes, synthetic construct, Eptatretus burgeri, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-07 Released: 2014-02-12 
• Deposition Author(s): Cheong, H.K., Kim, H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.268 
• R-Value Work: 0.205 

Starting Model: experimental

Literature

Modular evolution and design of the protein binding interface

Lee, J., Kim, H.J., Yang, C., Choi, J., Kyeong, H., Yuk, J., Park, K., Kim, Y.J., Heu, W., Lee, S., Kim, D., Jo, E.K., Cheong, H.K., Kim, H.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 98.51 kDa 
• Atom Count: 6,751 
• Modelled Residue Count: 830 
• Deposited Residue Count: 870 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Internalin B,REPEAT MODULES,Variable lymphocyte receptor B	A, B	267	Listeria monocytogenes, synthetic construct, Eptatretus burgeri This entity is chimeric	Mutation(s): 0
UniProt
Find proteins for Q4G1L3 (Eptatretus burgeri) Explore Q4G1L3  Go to UniProtKB:  Q4G1L3
Find proteins for A4L9V2 (Listeria monocytogenes) Explore A4L9V2  Go to UniProtKB:  A4L9V2
UniProt Groups	Q4G1L3A4L9V2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-6	C, D	168	Homo sapiens	Mutation(s): 0  Gene Names: IL6, IFNB2
UniProt & NIH Common Fund Data Resources
Find proteins for P05231 (Homo sapiens) Explore P05231  Go to UniProtKB:  P05231
PHAROS:  P05231 GTEx:  ENSG00000136244

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.268 
• R-Value Work: 0.205 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.319	α = 90
b = 134.001	β = 90
c = 148.722	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Cheong, H.K., Kim, H.J.

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references, Source and taxonomy
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary