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4e3c

X-ray crystal structure of human IKK2 in an active conformation

Method: X-RAY DIFFRACTION Dmax: 187.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Inhibitor of nuclear factor kappa-B kinase subunit beta

Homo sapiens

UniProt O14920

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 11–669 Chain F； UniProt 11–669 Fragment：UNP Residues 11-669 Mutation：S177E, S181E No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1.2M sodium malonate, 250mM ammonium acetate, 10mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.98 Å R-free 0.299
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 11–669 Chain C； UniProt 11–669 Fragment：UNP Residues 11-669 Mutation：S177E, S181E No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1.2M sodium malonate, 250mM ammonium acetate, 10mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.98 Å R-free 0.299
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 11–669 Chain E； UniProt 11–669 Fragment：UNP Residues 11-669 Mutation：S177E, S181E No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；1.2M sodium malonate, 250mM ammonium acetate, 10mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.98 Å R-free 0.299

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4E3C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3BRT NEMO/IKK association domain structure Deposited 2007-12-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 701–730（30 aa） Fragment：Fusion protein consists of UNP residues 701-730 of IKK-B and nemo-binding domain of IKK-A
Chain C 701–730（30 aa） Fragment：Fusion protein consists of UNP residues 701-730 of IKK-B and nemo-binding domain of IKK-A
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions microbatch under oil；pH 8；298 K；35% Peg 8K, 0.1M Tris pH 8, 0.2M Ammonium Chloride, 10mM Dithiothreitol., microbatch under oil, temperature 298K
Resolution 2.25 Å R-free 0.282
3BRT NEMO/IKK association domain structure Deposited 2007-12-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 701–730（30 aa） Fragment：Fusion protein consists of UNP residues 701-730 of IKK-B and nemo-binding domain of IKK-A
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions microbatch under oil；pH 8；298 K；35% Peg 8K, 0.1M Tris pH 8, 0.2M Ammonium Chloride, 10mM Dithiothreitol., microbatch under oil, temperature 298K
Resolution 2.25 Å R-free 0.282
3BRT NEMO/IKK association domain structure Deposited 2007-12-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 701–730（30 aa） Fragment：Fusion protein consists of UNP residues 701-730 of IKK-B and nemo-binding domain of IKK-A
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions microbatch under oil；pH 8；298 K；35% Peg 8K, 0.1M Tris pH 8, 0.2M Ammonium Chloride, 10mM Dithiothreitol., microbatch under oil, temperature 298K
Resolution 2.25 Å R-free 0.282
3BRT NEMO/IKK association domain structure Deposited 2007-12-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 701–730（30 aa） Fragment：Fusion protein consists of UNP residues 701-730 of IKK-B and nemo-binding domain of IKK-A
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions microbatch under oil；pH 8；298 K；35% Peg 8K, 0.1M Tris pH 8, 0.2M Ammonium Chloride, 10mM Dithiothreitol., microbatch under oil, temperature 298K
Resolution 2.25 Å R-free 0.282
3BRT NEMO/IKK association domain structure Deposited 2007-12-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 701–730（30 aa） Fragment：Fusion protein consists of UNP residues 701-730 of IKK-B and nemo-binding domain of IKK-A
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions microbatch under oil；pH 8；298 K；35% Peg 8K, 0.1M Tris pH 8, 0.2M Ammonium Chloride, 10mM Dithiothreitol., microbatch under oil, temperature 298K
Resolution 2.25 Å R-free 0.282
3BRV NEMO/IKKb association domain structure Deposited 2007-12-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 701–745（45 aa） Fragment：NEMO-binding
Chain C 701–745（45 aa） Fragment：NEMO-binding
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% Peg 4K, 0.1M Tris pH 8.5, 0.2M MgCl2, 10mM DTT, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.294
3BRV NEMO/IKKb association domain structure Deposited 2007-12-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 701–745（45 aa） Fragment：NEMO-binding
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% Peg 4K, 0.1M Tris pH 8.5, 0.2M MgCl2, 10mM DTT, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.294
3BRV NEMO/IKKb association domain structure Deposited 2007-12-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 701–745（45 aa） Fragment：NEMO-binding
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% Peg 4K, 0.1M Tris pH 8.5, 0.2M MgCl2, 10mM DTT, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.294
3BRV NEMO/IKKb association domain structure Deposited 2007-12-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 701–745（45 aa） Fragment：NEMO-binding
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% Peg 4K, 0.1M Tris pH 8.5, 0.2M MgCl2, 10mM DTT, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.294
3BRV NEMO/IKKb association domain structure Deposited 2007-12-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 701–745（45 aa） Fragment：NEMO-binding
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% Peg 4K, 0.1M Tris pH 8.5, 0.2M MgCl2, 10mM DTT, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.20 Å R-free 0.294
4KIK Human IkB kinase beta Deposited 2013-05-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–664（663 aa）
Chain B 2–664（663 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) KSA K-252A × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.83 Å R-free 0.236
8OMV Crystal structure of the constitutively active S117E/S181E mutant of human IKK2 Deposited 2023-03-31 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–669（669 aa）
Chain B 1–669（669 aa）
Mutation：S177E, S181E Mutation：S177E, S181E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6M (NH4)2SO4, 0.1M Bis-Tris HCl pH 6.5, 10% 2-propanol
Resolution 4.16 Å R-free 0.299
8OMV Crystal structure of the constitutively active S117E/S181E mutant of human IKK2 Deposited 2023-03-31 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–669（669 aa）
Chain D 1–669（669 aa）
Mutation：S177E, S181E Mutation：S177E, S181E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6M (NH4)2SO4, 0.1M Bis-Tris HCl pH 6.5, 10% 2-propanol
Resolution 4.16 Å R-free 0.299
8OMV Crystal structure of the constitutively active S117E/S181E mutant of human IKK2 Deposited 2023-03-31 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–669（669 aa）
Mutation：S177E, S181E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6M (NH4)2SO4, 0.1M Bis-Tris HCl pH 6.5, 10% 2-propanol
Resolution 4.16 Å R-free 0.299

4 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IKKB_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 11–669； UniProt 11–669 Author chain B； PDBConstruct 11–669； UniProt 11–669 Author chain C； PDBConstruct 11–669； UniProt 11–669 Author chain D； PDBConstruct 11–669； UniProt 11–669 Author chain E； PDBConstruct 11–669； UniProt 11–669 Author chain F； PDBConstruct 11–669； UniProt 11–669

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4e3c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4e3c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4e3c
Deposition date deposition_date2012-03-09
Structure title titleX-ray crystal structure of human IKK2 in an active conformation
Keywords keywordsKanase, auto-phosphorylation, NEMO binding, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier60.33 Å
Radius of gyration Rg (electron density) rg_electron60.08 Å
Forward intensity I(0) i02693430000.00
Molecular weight molecular_weight433790.0 kDa
Excluded volume excluded_volume542930 ų
Envelope volume envelope_volume882760 ų
Hydration-shell volume shell_volume123480 ų
Envelope diameter envelope_diameter197.5 Å
Shell Rg shell_rg62.72 Å
Envelope Rg envelope_rg57.24 Å
Shape Rg shape_rg60.11 Å
Total Rg total_rg60.06 Å
Total atoms total_atoms30416
Residues n_residues3752
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax187.1 Å
Rg (real space) rg_real59.95 Å
Rg uncertainty (real space) rg_real_error1.78 Å
I(0) (real space) i0_real2.6930e+09
I(0) uncertainty (real space) i0_real_error5.6350e+07
Rg (reciprocal space) rg_reciprocal60.63 Å
I(0) (reciprocal space) i0_reciprocal2696000000.0000
Solution quality estimate total_estimate0.8724
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary79.2 Å
Skewness Skewness skewness0.070
Kurtosis Kurtosis kurtosis-0.405
Angular range angular_range— – 0.1300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha109100000.0000
Real-space data points n_real_points27
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.670
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id4e3cA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4e3cA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4e3cA03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily250 —
Domain ID domain_id4e3cB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4e3cB02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4e3cB03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily250 —
Domain ID domain_id4e3cC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4e3cC02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4e3cC03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily250 —
Domain ID domain_id4e3cD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4e3cD02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4e3cD03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily250 —
Domain ID domain_id4e3cE01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4e3cE02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4e3cE03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily250 —
Domain ID domain_id4e3cF01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id4e3cF02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4e3cF03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily250 —
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8. Citations (1)

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9. Files and Curves (10)