8FO3 | pdb_00008fo3

Structure of full-length amyloidogenic immunoglobulin light chain H9 in complex with (E)-3-nitro-4-(2-(2-phenylpropylidene)hydrazineyl)benzenesulfonamide

PDB DOI: https://doi.org/10.2210/pdb8FO3/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.280 (Depositor), 0.284 (DCC)
R-Value Work:
0.229 (Depositor), 0.235 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 273.27 kDa
Atom Count: 20,516
Modeled Residue Count: 2,553
Deposited Residue Count: 2,592
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H9 immunoglobulin light chain	A B C D E [auth G] A, B, C, D, E [auth G], F [auth H], G [auth I], H [auth J], I [auth E], J [auth F], K, L	216	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y4K (Subject of Investigation/LOI) Query on Y4K Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain W [auth K] SDF format, chain U [auth E] SDF format, chain T [auth I] SDF format, chain Q [auth G] SDF format, chain P [auth C] MOL2 format, chain M [auth A] MOL2 format, chain W [auth K] MOL2 format, chain U [auth E] MOL2 format, chain T [auth I] MOL2 format, chain Q [auth G] MOL2 format, chain P [auth C] mmCIF format, chain M [auth A] mmCIF format, chain W [auth K] mmCIF format, chain U [auth E] mmCIF format, chain T [auth I] mmCIF format, chain Q [auth G] mmCIF format, chain P [auth C]	M [auth A] P [auth C] Q [auth G] T [auth I] U [auth E] M [auth A], P [auth C], Q [auth G], T [auth I], U [auth E], W [auth K]	3-nitro-4-{2-[(2S)-2-phenylpropyl]hydrazin-1-yl}benzene-1-sulfonamide C₁₅ H₁₈ N₄ O₄ S NSSXWTMELVHXJK-LLVKDONJSA-N		Interactions Focus chain M [auth A] Focus chain P [auth C] Focus chain Q [auth G] Focus chain T [auth I] Focus chain U [auth E] Focus chain W [auth K] Interactions & Density Focus chain M [auth A] Focus chain P [auth C] Focus chain Q [auth G] Focus chain T [auth I] Focus chain U [auth E] Focus chain W [auth K]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain R [auth G] SDF format, chain X [auth K] SDF format, chain V [auth E] SDF format, chain S [auth H] SDF format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth G] MOL2 format, chain X [auth K] MOL2 format, chain V [auth E] MOL2 format, chain S [auth H] MOL2 format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth G] mmCIF format, chain X [auth K] mmCIF format, chain V [auth E] mmCIF format, chain S [auth H] mmCIF format, chain N [auth A]	N [auth A] O [auth B] R [auth G] S [auth H] V [auth E] N [auth A], O [auth B], R [auth G], S [auth H], V [auth E], X [auth K]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain N [auth A] Focus chain O [auth B] Focus chain R [auth G] Focus chain S [auth H] Focus chain V [auth E] Focus chain X [auth K] Interactions & Density Focus chain N [auth A] Focus chain O [auth B] Focus chain R [auth G] Focus chain S [auth H] Focus chain V [auth E] Focus chain X [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.280 (Depositor), 0.284 (DCC)
R-Value Work: 0.229 (Depositor), 0.235 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.141	α = 106.31
b = 95.655	β = 92.93
c = 125.918	γ = 90.16

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-24

Deposition Author(s):

Yan, N.L.

Wilson, I.A.

Kelly, J.W.

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 (Full details and data files)

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
Version 1.3: 2026-04-15
Changes: Data collection, Derived calculations, Structure summary