5EBZ

Crystal structure of human IKK1

PDB DOI: https://doi.org/10.2210/pdb5EBZ/pdb

Classification: Transferase/transferase inhibitor
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2015-10-20 Released: 2016-11-02
Deposition Author(s): Polley, S., Passos, D., Huang, D., Biswas, T., Verma, I., Lyumkis, D., Ghosh, G.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.50 Å
R-Value Free: 0.276
R-Value Work: 0.238
R-Value Observed: 0.238

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 933.78 kDa
Atom Count: 65,132
Modelled Residue Count: 7,860
Deposited Residue Count: 7,860
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inhibitor of nuclear factor kappa-B kinase subunit alpha	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	655	Homo sapiens	Mutation(s): 3 Gene Names: CHUK, IKKA, TCF16 EC: 2.7.11.10
UniProt & NIH Common Fund Data Resources
Find proteins for O15111 (Homo sapiens) Explore O15111 Go to UniProtKB: O15111
PHAROS: O15111 GTEx: ENSG00000213341
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15111
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2,3-di-O-sulfo-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-2,4-di-O-sulfo-alpha-D-glucopyranose	AA [auth a], BA [auth b], DA [auth d], EA [auth e], FA [auth f], AA [auth a], BA [auth b], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], JA [auth j], KA [auth k], LA [auth l], M, MA [auth m], N, NA [auth n], P, Q, R, S, U, V, W, X, Y, Z	3		N/A	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain M Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G32438WU GlyCosmos: G32438WU

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4-bis(oxidanyl)-5-oxidanylsulfanyloxy-oxan-3-yl] hydrogen sulfate-(1-6)-(2S,3R,4R,5S,6R)-6-(hydroxymethyl)-5-oxidanylsulfanyloxy-oxane-2,3,4-triol-(1-6)-2-O-sulfo-alpha-D-glucopyranose-(1-6)-[(2R,3R,4R,5R,6S)-2-(hydroxymethyl)-5,6-bis(oxidanyl)-3-oxidanylsulfanyloxy-oxan-4-yl] hydrogen sulfate-(1-6)-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-2,5-bis(oxidanyl)-4-oxidanylsulfanyloxy-oxan-3-yl] hydrogen sulfate-(1-6)-[(2R,3R,4R,5R,6S)-2-(hydroxymethyl)-5,6-bis(oxidanyl)-3-oxidanylsulfanyloxy-oxan-4-yl] hydrogen sulfate-(1-6)-2,4-di-O-sulfo-alpha-D-glucopyranose	CA [auth c], IA [auth i], O, T	7	N/A	N/A	Interactions Focus chain CA [auth c] Focus chain IA [auth i] Focus chain O Focus chain T Interactions & Density Focus chain CA [auth c] Focus chain IA [auth i] Focus chain O Focus chain T
Glycosylation Resources
GlyTouCan: G51196UN GlyCosmos: G51196UN

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5TL Query on 5TL Download Ideal Coordinates CCD File SDF format, chain OA [auth A] SDF format, chain PA [auth B] SDF format, chain QA [auth C] SDF format, chain RA [auth D] SDF format, chain SA [auth E] SDF format, chain TA [auth F] SDF format, chain UA [auth G] SDF format, chain VA [auth H] SDF format, chain WA [auth I] SDF format, chain XA [auth J] SDF format, chain YA [auth K] SDF format, chain ZA [auth L] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth E] MOL2 format, chain TA [auth F] MOL2 format, chain UA [auth G] MOL2 format, chain VA [auth H] MOL2 format, chain WA [auth I] MOL2 format, chain XA [auth J] MOL2 format, chain YA [auth K] MOL2 format, chain ZA [auth L]	OA [auth A] PA [auth B] QA [auth C] RA [auth D] SA [auth E] OA [auth A], PA [auth B], QA [auth C], RA [auth D], SA [auth E], TA [auth F], UA [auth G], VA [auth H], WA [auth I], XA [auth J], YA [auth K], ZA [auth L]	2-azanyl-5-phenyl-3-(4-sulfamoylphenyl)benzamide C₁₉ H₁₇ N₃ O₃ S IVJPEEHVYKDQEO-UHFFFAOYSA-N		Interactions Focus chain OA [auth A] Focus chain PA [auth B] Focus chain QA [auth C] Focus chain RA [auth D] Focus chain SA [auth E] Focus chain TA [auth F] Focus chain UA [auth G] Focus chain VA [auth H] Focus chain WA [auth I] Focus chain XA [auth J] Focus chain YA [auth K] Focus chain ZA [auth L] Interactions & Density Focus chain OA [auth A] Focus chain PA [auth B] Focus chain QA [auth C] Focus chain RA [auth D] Focus chain SA [auth E] Focus chain TA [auth F] Focus chain UA [auth G] Focus chain VA [auth H] Focus chain WA [auth I] Focus chain XA [auth J] Focus chain YA [auth K] Focus chain ZA [auth L]

Binding Affinity Annotations
ID	Source	Binding Affinity
5TL	BindingDB: 5EBZ	IC50: 1000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.50 Å
R-Value Free: 0.276
R-Value Work: 0.238
R-Value Observed: 0.238
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.51	α = 90
b = 186.94	β = 98.84
c = 275.83	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-11-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA141722

Revision History (Full details and data files)

Version 1.0: 2016-11-02
Type: Initial release
Version 1.1: 2016-12-21
Changes: Database references
Version 1.2: 2017-09-06
Changes: Author supporting evidence
Version 1.3: 2019-12-04
Changes: Author supporting evidence, Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations, Structure summary

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Help and Resources

5EBZ

Crystal structure of human IKK1

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)