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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	transcription factor inhibitor I-kappa-B-beta × 1 （Q60778） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Transcription factor p65 × 2 （Q04207） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

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. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1k3z__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1k3z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1k3z__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	25.05 Å
Rg (electron density)	24.29 Å
Total Rg	25.03 Å
Atom count	3670
Residues	469
Excluded volume	64657 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1k3z__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. 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

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism 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

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism 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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6. 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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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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1k3z__assembly_1__model_1

1k3z__assembly_1__model_1 | I(q)

1k3z__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

transcription factor inhibitor I-kappa-B-beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1k3z__assembly_1__model_1

1k3z__assembly_1__model_1 | I(q)

1k3z__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)