SAXSdb — 1k3z

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

Transcription factor p65

Mus musculus

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 191–326 Chain B； UniProt 191–326	Fragment：p65 dimerization domain	transcription factor inhibitor I-kappa-B-beta × 1 （Q60778）	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.50 Å R-free 0.256

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 1K3Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BFT STRUCTURE OF NF-KB P65 HOMODIMER BOUND TO A KB SITE Deposited 1997-09-12	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 191–291（101 aa） Fragment：DIMERIZATION DOMAIN Chain B 191–291（101 aa） Fragment：DIMERIZATION DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.294
1IKN IKAPPABALPHA/NF-KAPPAB COMPLEX Deposited 1998-11-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 19–304（286 aa） Fragment：N-TERMINAL AND DIMERIZATION DOMAINS	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.00	Resolution 2.30 Å R-free 0.277
1LE5 Crystal structure of a NF-kB heterodimer bound to an IFNb-kB Deposited 2002-04-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 20–291（272 aa） Fragment：p65 RHR	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；50 mM Na acatate, 50mM CaCl2, 1.0 mM Na spermine, 8% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.75 Å R-free 0.293
1LE5 Crystal structure of a NF-kB heterodimer bound to an IFNb-kB Deposited 2002-04-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain E 20–291（272 aa） Fragment：p65 RHR	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；50 mM Na acatate, 50mM CaCl2, 1.0 mM Na spermine, 8% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.75 Å R-free 0.293
1LE9 Crystal structure of a NF-kB heterodimer bound to the Ig/HIV-kB siti Deposited 2002-04-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 20–291（272 aa） Fragment：p65 RHR	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；PEG 3350, CaCl2, Na acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 110K	Resolution 3.00 Å R-free 0.305
1LE9 Crystal structure of a NF-kB heterodimer bound to the Ig/HIV-kB siti Deposited 2002-04-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain E 20–291（272 aa） Fragment：p65 RHR	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；PEG 3350, CaCl2, Na acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 110K	Resolution 3.00 Å R-free 0.305
1LEI The kB DNA sequence from the HLV-LTR functions as an allosteric regulator of HIV transcription Deposited 2002-04-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 20–291（272 aa） Fragment：p65 RHR	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；pH 6.5；291 K；PEG 3350, CaCl2, sodium spermine, pH 6.5, SMALL TUBES, temperature 291K	Resolution 2.70 Å R-free 0.284
1MY5 NF-kappaB p65 subunit dimerization domain homodimer Deposited 2002-10-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 191–304（114 aa） Fragment：residues 191-304 (dimerization domain) Chain B 191–304（114 aa） Fragment：residues 191-304 (dimerization domain)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1M sodium HEPES, 0.2M sodium tartrate, 2M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.221
1MY7 NF-kappaB p65 subunit dimerization domain homodimer N202R mutation Deposited 2002-10-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 191–304（114 aa） Fragment：residues 191 - 304 (dimerization domain) Chain B 191–304（114 aa） Fragment：residues 191 - 304 (dimerization domain)	Mutation：N202R Mutation：N202R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.l M sodium HEPES, 0.2 M sodium tartrate, 2 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.49 Å R-free 0.247
1OY3 CRYSTAL STRUCTURE OF AN IKBBETA/NF-KB P65 HOMODIMER COMPLEX Deposited 2003-04-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 191–326（136 aa） Fragment：p65 dimerization domain Chain C 191–326（136 aa） Fragment：p65 dimerization domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；291 K；PEG 8000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.05 Å R-free 0.247
1RAM A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER Deposited 1997-11-22	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 A 19–291（273 aa） Fragment：P65 SUBUNIT, RESIDUES 19 - 291 Chain B 19–291（273 aa） Fragment：P65 SUBUNIT, RESIDUES 19 - 291	Not recorded	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；crystallized from PEG 3350, CACL2, BETA-OCTYL GLUCOPYRANOSIDE, HEPES and GLYCEROL, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 291.00K	Resolution 2.70 Å R-free 0.324
1VKX CRYSTAL STRUCTURE OF THE NFKB P50/P65 HETERODIMER COMPLEXED TO THE IMMUNOGLOBULIN KB DNA Deposited 1997-09-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 19–291（273 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；pH 5.50, VAPOR DIFFUSION, HANGING DROP	Resolution 2.90 Å R-free 0.320
2I9T Structure of NF-kB p65-p50 heterodimer bound to PRDII element of B-interferon promoter Deposited 2006-09-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 19–291（273 aa） Fragment：residues 19-291	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；293 K；8% PEG 5K monomethylether, 200mM sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.60	Resolution 2.80 Å R-free 0.288
2RAM A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER Deposited 1997-11-23	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 A 19–291（273 aa） Fragment：P65 RESIDUES 19 - 291 Chain B 19–291（273 aa） Fragment：P65 RESIDUES 19 - 291	Not recorded	DTV (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.40 Å R-free 0.308
5U01 Cooperative DNA binding by two RelA dimers Deposited 2016-11-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: hexameric	Chain A 19–291（273 aa） Fragment：UNP residues 19-291 Chain B 19–291（273 aa） Fragment：UNP residues 19-291 Chain C 19–291（273 aa） Fragment：UNP residues 19-291 Chain D 19–291（273 aa） Fragment：UNP residues 19-291	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；293 K；Nacit 5.5 100mM, CaCl2 10mM, DTT 10mM, PEG 3350 15%.	Resolution 2.50 Å R-free 0.274
6GGR Crystal structure of Salmonella zinc metalloprotease effector GtgA in complex with p65 Deposited 2018-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 20–188（169 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Crystallyzation conditions: 0.1 M Tris pH 8.3, 0.5 M LiCl and 32.5% (w/v) PEG 6000	Resolution 2.10 Å R-free 0.252
8U9L Crystal Structure of RelA-cRel chimera complex with DNA Deposited 2023-09-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 19–98（80 aa） Chain A 191–291（101 aa） Chain B 19–98（80 aa） Chain B 191–291（101 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium/Potassium phosphate 0.1M Bis Tris propane pH 6.5 20% PEG 3350 10mM DTT 0.5% BOG	Resolution 3.09 Å R-free 0.329
8U9L Crystal Structure of RelA-cRel chimera complex with DNA Deposited 2023-09-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain G 19–98（80 aa） Chain G 191–291（101 aa） Chain H 19–98（80 aa） Chain H 191–291（101 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium/Potassium phosphate 0.1M Bis Tris propane pH 6.5 20% PEG 3350 10mM DTT 0.5% BOG	Resolution 3.09 Å R-free 0.329
8U9L Crystal Structure of RelA-cRel chimera complex with DNA Deposited 2023-09-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain K 19–98（80 aa） Chain K 191–291（101 aa） Chain L 19–98（80 aa） Chain L 191–291（101 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium/Potassium phosphate 0.1M Bis Tris propane pH 6.5 20% PEG 3350 10mM DTT 0.5% BOG	Resolution 3.09 Å R-free 0.329
8U9L Crystal Structure of RelA-cRel chimera complex with DNA Deposited 2023-09-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain O 19–98（80 aa） Chain O 191–291（101 aa） Chain P 19–98（80 aa） Chain P 191–291（101 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2M Sodium/Potassium phosphate 0.1M Bis Tris propane pH 6.5 20% PEG 3350 10mM DTT 0.5% BOG	Resolution 3.09 Å R-free 0.329
9BDU NF-kappaB RelA homo-dimer bound to AT-centric kappaB DNA Deposited 2024-04-12	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 A 19–304（286 aa） Fragment：residues 19-304 Chain B 19–304（286 aa） Fragment：residues 19-304	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, MES, beta-octylglucoside, spermine	Resolution 2.03 Å R-free 0.273
9BDV NF-kappaB RelA homo-dimer bound to TA-centric kappaB DNA Deposited 2024-04-12	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 A 19–304（286 aa） Fragment：residues 19-304 Chain B 19–304（286 aa） Fragment：residues 19-304	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, MES, Spermine, beta-octylglucoside	Resolution 1.90 Å R-free 0.230
9BDW NF-kappaB RelA homo-dimer bound to GC-centric kappaB DNA Deposited 2024-04-12	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 A 19–304（286 aa） Fragment：residues 19-304 Chain B 19–304（286 aa） Fragment：residues 19-304	Not recorded	SO4 SULFATE ION × 5 BOG octyl beta-D-glucopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, MES, Spermine, beta-octylglucoside	Resolution 1.87 Å R-free 0.227
9BDX NF-kappaB RelA homo-dimer bound to CG-centric kappaB DNA Deposited 2024-04-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 19–304（286 aa） Fragment：residues 19-304 Chain B 19–304（286 aa） Fragment：residues 19-304	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, MES, Spermine, beta-octylglucoside	Resolution 3.60 Å R-free 0.374
9E6W NF-kappaB RelA homo-dimer bound to a kappaB site of Cxcl2 gene Deposited 2024-10-31	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 19–304（286 aa） Fragment：residues 19-304 Chain B 19–304（286 aa） Fragment：residues 19-304	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Tris HCl 25mM pH 7.5, NaCl 50 mM, DTT 1 mM, MES 50 mM pH 5.5, CaCl2 2 mM, Spermidine 1 mM, b-D-octylglucopyranoside 0.05%, Ammonium chloride 50 mM, PEG3350 14%	Resolution 2.04 Å R-free 0.283

20 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TF65_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 191–326 Author chain B； PDBConstruct 1–136； UniProt 191–326

transcription factor inhibitor I-kappa-B-beta

Mus musculus

UniProt Q60778

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 50–331	Mutation：S312E, S313E, S314E, S316E, S318E	Transcription factor p65 × 2 （Q04207）	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.50 Å R-free 0.256

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 1K3Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OY3 CRYSTAL STRUCTURE OF AN IKBBETA/NF-KB P65 HOMODIMER COMPLEX Deposited 2003-04-03	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 50–331（282 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；291 K；PEG 8000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.05 Å R-free 0.247

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IKBB_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–282； UniProt 50–331

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	1k3z
Deposition date deposition_date	2001-10-04
Structure title title	X-ray crystal structure of the IkBb/NF-kB p65 homodimer complex
Keywords keywords	protein-protein complex, transcription factors, nuclear localization, 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	25.05 Å
Radius of gyration Rg (electron density) rg_electron	24.29 Å
Forward intensity I(0) i0	48063900.00
Molecular weight molecular_weight	52164.0 kDa
Excluded volume excluded_volume	64657 Å³
Envelope volume envelope_volume	79243 Å³
Hydration-shell volume shell_volume	27178 Å³
Envelope diameter envelope_diameter	86.0 Å
Shell Rg shell_rg	31.25 Å
Envelope Rg envelope_rg	24.28 Å
Shape Rg shape_rg	24.30 Å
Total Rg total_rg	25.03 Å
Total atoms total_atoms	3670
Residues n_residues	469
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	82.0 Å
Rg (real space) rg_real	24.98 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	4.8060e+07
I(0) uncertainty (real space) i0_real_error	6.7170e+05
Rg (reciprocal space) rg_reciprocal	25.01 Å
I(0) (reciprocal space) i0_reciprocal	48060000.0000
Solution quality estimate total_estimate	0.8933
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	80.7 Å
Skewness Skewness skewness	0.267
Kurtosis Kurtosis kurtosis	-0.342
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11970000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.989

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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	Transcription factor p65
Molecular weight formula_weight	15743.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3769

TAELKICRVNRNSGSCLGGDEIFLLCDKVQKEDIEVYFTGPGWEARGSFSQADVHRQVAIVFRTPPYADPSLQAPVRVSMQLRRPSDRELSEPMEFQYLPDTDDRHRIEEKRKRTYETFKSIMKKSPFNGPTEPRP

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	transcription factor inhibitor I-kappa-B-beta
Molecular weight formula_weight	30537.6 kDa
Mutation mutation	S312E, S313E, S314E, S316E, S318E
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

VFGYVTEDGDTALHLAVIHQHEPFLDFLLGFSAGHEYLDLQNDLGQTALHLAAILGEASTVEKLYAAGAGVLVAERGGHTALHLACRVRAHTCACVLLQPRPSHPRDASDTYLTQSQDCTPDTSHAPAAVDSQPNPENEEEPRDEDWRLQLEAENYDGHTPLHVAVIHKDAEMVRLLRDAGADLNKPEPTCGRTPLHLAVEAQAASVLELLLKAGADPTARMYGGRTPLGSALLRPNPILARLLRAHGAPEPEDGGDKLSPCEEEGEDEDSDNRDEGDEYDD

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

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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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1k3za_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.1 — NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain

Domain ID domain_id	d1k3zb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.1 — NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain

Domain ID domain_id	d1k3zd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.211 — beta-hairpin-alpha-hairpin repeat
Superfamily Superfamily superfamily	d.211.1 — Ankyrin repeat
Family Family family	d.211.1.1 — Ankyrin repeat

CATH v4.4 (3 domains)

Domain ID domain_id	1k3zA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1k3zB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1k3zD00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

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8. Citations (1)

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Unit-cell length a length_a	46.400 Å
Unit-cell length b length_b	48.920 Å
Unit-cell length c length_c	59.470 Å
Unit-cell angle α angle_alpha	95.17 °
Unit-cell angle β angle_beta	91.80 °
Unit-cell angle γ angle_gamma	105.45 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.1810
R_free r_free	0.2560

fit	/app/data/saxs_computation/k3/1k3z/1k3z.fit
pddf	/app/data/pr_computation/k3/1k3z/1k3z.pr.out
profile	/app/data/saxs_computation/k3/1k3z/1k3z.dat

X-ray crystal structure of the IkBb/NF-kB p65 homodimer complex

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

Transcription factor p65

State in the Current Structure

Other States of the Same Protein in the Database

transcription factor inhibitor I-kappa-B-beta

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)