8FO4 | pdb_00008fo4

Structure of full-length amyloidogenic immunoglobulin light chain H9 in complex with 6-methyl-2-(2-((1E,2E)-3-(2-nitrophenyl)allylidene)hydrazineyl)pyrimidin-4-ol

• PDB DOI: https://doi.org/10.2210/pdb8FO4/pdb

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


• Deposited: 2022-12-29 Released: 2023-05-24 
• Deposition Author(s): Yan, N.L., Wilson, I.A., Kelly, J.W.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.238 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of Diaryl Hydrazone and Sulfone Stabilizers in Complex with an Amyloidogenic Light Chain Reveal an Alternate Ligand-Binding Cavity

Yan, N.L., Wilson, I.A., Kelly, J.W.

(2023) Isr J Chem 

• DOI: https://doi.org/10.1002/ijch.202300002

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.99 kDa 
• Atom Count: 7,079 
• Modeled Residue Count: 844 
• Deposited Residue Count: 864 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H9 immunoglobulin light chain	A, B, C, D	216	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y4Q (Subject of Investigation/LOI)	E [auth A], H [auth D]	6-methyl-2-{2-[(1E)-3-(2-nitrophenyl)prop-1-en-1-yl]hydrazinyl}pyrimidin-4(5H)-one C14 H15 N5 O3 RQPQHPRGYAGHMJ-XBXARRHUSA-N
PO4	F [auth A], G [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.238 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.495	α = 84.76
b = 63.19	β = 87.7
c = 86.978	γ = 81.18

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Yan, N.L., Wilson, I.A., Kelly, J.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL157566
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL154732

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary