SAXSdb — 8tqd

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nuclear factor NF-kappa-B p105 subunit

Homo sapiens

UniProt P19838

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 40–245	Not recorded	JMR 1-(2-bromo-4-chlorophenyl)-N-{(3S)-1-[(E)-iminomethyl]pyrrolidin-3-yl}methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1 M Citrate pH5.0, 20%w/v PEG 6000	Resolution 2.02 Å R-free 0.227

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 8TQD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1MDI HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERMEDIATE BETWEEN MUTANT HUMAN THIOREDOXIN AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN NFKB Deposited 1995-02-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 53–65（13 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1MDJ HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERMEDIATE BETWEEN HUMAN THIOREDOXIN (C35A, C62A, C69A, C73A) MUTANT AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN NFKB (RESIDUES 56-68 OF THE P50 SUBUNIT OF NFKB) Deposited 1995-02-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 53–65（13 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1MDK HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERMEDIATE BETWEEN HUMAN THIOREDOXIN (C35A, C62A, C69A, C73A) MUTANT AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN NFKB (RESIDUES 56-68 OF THE P50 SUBUNIT OF NFKB) Deposited 1995-02-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 53–65（13 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1NFI I-KAPPA-B-ALPHA/NF-KAPPA-B COMPLEX Deposited 1998-08-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 248–354（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.0	Resolution 2.70 Å R-free 0.265
1NFI I-KAPPA-B-ALPHA/NF-KAPPA-B COMPLEX Deposited 1998-08-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 248–354（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5.0	Resolution 2.70 Å R-free 0.265
1SVC NFKB P50 HOMODIMER BOUND TO DNA Deposited 1995-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain P 2–366（365 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 2.60 Å R-free 0.286
2DBF Solution structure of the Death domain in human Nuclear factor NF-kappa-B p105 subunit Deposited 2005-12-15	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 806–893（88 aa） Fragment：DEATH DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure AMBIENT NMR sample composition 1mM protein; 20mM d-tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2O61 Crystal Structure of NFkB, IRF7, IRF3 bound to the interferon-b enhancer Deposited 2006-12-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 40–352（313 aa） Fragment：RHR region	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；100 mM HEPES, pH 7.0, 15% (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.80 Å R-free 0.278
3GUT Crystal structure of a higher-order complex of p50:RelA bound to the HIV-1 LTR Deposited 2009-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 41–352（312 aa） Fragment：UNP residues 41-352 Chain D 41–352（312 aa） Fragment：UNP residues 41-352	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；289 K；50mM BTP pH 6.3, 50mM CaCl2, 7% w/v PEG 3000, 1mM Spermine, 10mM DTT, 8% v/v Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.59 Å R-free 0.301
3GUT Crystal structure of a higher-order complex of p50:RelA bound to the HIV-1 LTR Deposited 2009-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain F 41–352（312 aa） Fragment：UNP residues 41-352 Chain H 41–352（312 aa） Fragment：UNP residues 41-352	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；289 K；50mM BTP pH 6.3, 50mM CaCl2, 7% w/v PEG 3000, 1mM Spermine, 10mM DTT, 8% v/v Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.59 Å R-free 0.301
7LEQ Structure of importin a2 bound to p50 NLS Deposited 2021-01-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 355–368（14 aa） Fragment：Nuclear localization signal motif, residues 355-368	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.6M sodium citrate, 100 Hepes pH 6.0	Resolution 2.24 Å R-free 0.219
7LET Structure of importin a2 bound to the p50- and p65-NLSs Deposited 2021-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 355–368（14 aa） Fragment：Nuclear localization signal motif, residues 355-368	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.6 Na Citrate, 100 mM HEPES pH 6	Resolution 2.40 Å R-free 0.241
7LF4 Structure of importin a3 bound to the p50- and p65-NLSs Deposited 2021-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 355–368（14 aa） Fragment：Nuclear localization signal motif, residues 355-368	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2 M ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 25% PEG 3350	Resolution 2.85 Å R-free 0.238
7LF4 Structure of importin a3 bound to the p50- and p65-NLSs Deposited 2021-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 355–368（14 aa） Fragment：Nuclear localization signal motif, residues 355-368	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2 M ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 25% PEG 3350	Resolution 2.85 Å R-free 0.238
7LFC Structure of importin a3 bound to p50 NLS Deposited 2021-01-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 355–368（14 aa） Fragment：Nuclear localization signal motif, residues 355-368	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2M potassium thiocyanate, 20% PEG3350, 0.1 M BIS-TRIS pH 6.5	Resolution 2.10 Å R-free 0.220
7RG4 Importin alpha2 in complex with p50 NLS Deposited 2021-07-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 151–190（40 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.7 M sodium citrate, 0.01M DTT, 0.1M sodium HEPES pH 7	Resolution 2.60 Å R-free 0.243

13 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NFKB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–207； UniProt 40–245

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8tqd
Deposition date deposition_date	2023-08-07
Structure title title	NF-Kappa-B1 Bound with a Covalent Inhibitor
Keywords keywords	Transcription factor, DNA binding protein, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.42 Å
Radius of gyration Rg (electron density) rg_electron	17.23 Å
Forward intensity I(0) i0	9504810.00
Molecular weight molecular_weight	22548.0 kDa
Excluded volume excluded_volume	28197 Å³
Envelope volume envelope_volume	33505 Å³
Hydration-shell volume shell_volume	16431 Å³
Envelope diameter envelope_diameter	61.8 Å
Shell Rg shell_rg	23.19 Å
Envelope Rg envelope_rg	17.66 Å
Shape Rg shape_rg	17.18 Å
Total Rg total_rg	18.36 Å
Total atoms total_atoms	1577
Residues n_residues	200
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	73.1 Å
Rg (real space) rg_real	18.34 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	9.5050e+06
I(0) uncertainty (real space) i0_real_error	1.4370e+05
Rg (reciprocal space) rg_reciprocal	18.35 Å
I(0) (reciprocal space) i0_reciprocal	9505000.0000
Solution quality estimate total_estimate	0.7102
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	23.0 Å
Skewness Skewness skewness	0.204
Kurtosis Kurtosis kurtosis	-0.372
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2133000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.460; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.851; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Nuclear factor NF-kappa-B p105 subunit
Molecular weight formula_weight	22738.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1713

GDGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	1-(2-bromo-4-chlorophenyl)-N-{(3S)-1-[(E)-iminomethyl]pyrrolidin-3-yl}methanesulfonamide
Molecular weight formula_weight	380.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

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8. Citations (1)

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Unit-cell length a length_a	57.210 Å
Unit-cell length b length_b	57.210 Å
Unit-cell length c length_c	71.850 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	3

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.020 Å
Low-resolution limit resolution_low	49.550 Å
R factor r_factor	0.1837
R_work r_work	0.1816
R_free r_free	0.2266

fit	/app/data/saxs_computation/tq/8tqd/8tqd.fit
pddf	/app/data/pr_computation/tq/8tqd/8tqd.pr.out
profile	/app/data/saxs_computation/tq/8tqd/8tqd.dat

NF-Kappa-B1 Bound with a Covalent Inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Nuclear factor NF-kappa-B p105 subunit

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction