8U7C

Engineered NEMO minimal IKK-binding domain

PDB DOI: https://doi.org/10.2210/pdb8U7C/pdb

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

Deposited: 2023-09-15 Released: 2025-01-22
Deposition Author(s): Kennedy, A.E., Pellegrini, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.44 Å
R-Value Free: 0.202
R-Value Work: 0.173
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

The structure of a NEMO construct engineered for screening reveals novel determinants of inhibition

Kennedy, A.E., Barczewski, A.H., Arnoldy, C.R., Pennington, J.P., Tiernan, K.A., HIdalgo, M.B., Reilly, C.C., Wongsri, T., Ragusa, M.J., Grigoryan, G., Mierke, D.F., Pellegrini, M.

(2025) Structure

DOI: https://doi.org/10.1016/j.str.2025.01.010

Macromolecule Content

Total Structure Weight: 35.65 kDa
Atom Count: 2,524
Modelled Residue Count: 245
Deposited Residue Count: 268
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered NEMO minimal IKK-binding domain	A, B, C, D	67	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain H [auth A] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain U [auth D] MOL2 format, chain H [auth A] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain U [auth D] mmCIF format, chain H [auth A] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	H [auth A], U [auth D], V [auth D], W [auth D], X [auth D]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain H [auth A] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain T [auth D] MOL2 format, chain L [auth B] MOL2 format, chain T [auth D] mmCIF format, chain L [auth B] mmCIF format, chain T [auth D]	L [auth B], T [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain T [auth D] Interactions & Density Focus chain L [auth B] Focus chain T [auth D]
ER3 Query on ER3 Download Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	ERBIUM (III) ION Er JHFPQYFEJICGKC-UHFFFAOYSA-N		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
TB Query on TB Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D]	E [auth A], O [auth D], P [auth D]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain O [auth D] Focus chain P [auth D]
PRO Query on PRO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B]	I [auth A], N [auth B]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Interactions & Density Focus chain I [auth A] Focus chain N [auth B]
9JE Query on 9JE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain S [auth D] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain S [auth D]	F [auth A], G [auth A], K [auth B], M [auth B], S [auth D]	pentane-1,5-diol C₅ H₁₂ O₂ ALQSHHUCVQOPAS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain S [auth D]
YT3 Query on YT3 Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain R [auth D] MOL2 format, chain J [auth B] MOL2 format, chain R [auth D] mmCIF format, chain J [auth B] mmCIF format, chain R [auth D]	J [auth B], R [auth D]	YTTRIUM (III) ION Y GRTBAGCGDOYUBE-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain R [auth D] Interactions & Density Focus chain J [auth B] Focus chain R [auth D]