SAXSdb — 1ubd

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

PROTEIN (YY1 ZINC FINGER DOMAIN)

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(APGPGPGPTPCPTPCPCPAPTPTPTPTPGPAPA PGPCPG)-3') ; × 1 ;DNA (5'-D(CPGPCPTPTPCPAPAPAPAPTPGPGPAPGPAPC PCPCPT)-3') ; × 1 ZINC ION × 4 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TYY1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–124； UniProt 293–414

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	1ubd
Deposition date deposition_date	1996-10-04
Structure title title	CO-CRYSTAL STRUCTURE OF HUMAN YY1 ZINC FINGER DOMAIN BOUND TO THE ADENO-ASSOCIATED VIRUS P5 INITIATOR ELEMENT
Keywords keywords	;TRANSCRIPTION INITIATION, INITIATOR ELEMENT, YY1, ZINC FINGER PROTEIN, DNA- PROTEIN RECOGNITION, COMPLEX (TRANSCRIPTION REGULATION-DNA), TRANSCRIPTION-DNA COMPLEX ;; TRANSCRIPTION/DNA
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.

1ubd__assembly_1__model_1

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

Download this curve (.dat)

1ubd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ubd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.39 Å
Rg (electron density)	19.84 Å
Total Rg	20.49 Å
Atom count	1722
Residues	154
Excluded volume	27932 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ubd__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 (5)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(APGPGPGPTPCPTPCPCPAPTPTPTPTPGPAPA PGPCPG)-3') ;
Molecular weight formula_weight	6165.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	1809

AGGGTCTCCATTTTGAAGCG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(CPGPCPTPTPCPAPAPAPAPTPGPGPAPGPAPC PCPCPT)-3') ;
Molecular weight formula_weight	6103.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

CGCTTCAAAATGGAGACCCT

Entity 3 Entity 3 polymer

Description description	PROTEIN (YY1 ZINC FINGER DOMAIN)
Molecular weight formula_weight	14189.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MEPRTIACPHKGCTKMFRDNSAMRKHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTGDRPYVCPFDGCNKKFAQSTNLKSHILTHAKAKNNQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	87

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ubdc1
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

Domain ID domain_id	d1ubdc2
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

Domain ID domain_id	d1ubdc3
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

Domain ID domain_id	d1ubdc4
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

CATH v4.4 (4 domains)

Domain ID domain_id	1ubdC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	1ubdC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	1ubdC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	1ubdC04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

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Unit-cell length a length_a	44.000 Å
Unit-cell length b length_b	65.700 Å
Unit-cell length c length_c	117.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	0.3300

CO-CRYSTAL STRUCTURE OF HUMAN YY1 ZINC FINGER DOMAIN BOUND TO THE ADENO-ASSOCIATED VIRUS P5 INITIATOR ELEMENT

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

PROTEIN (YY1 ZINC FINGER DOMAIN)

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

1ubd__assembly_1__model_1

1ubd__assembly_1__model_1 | I(q)

1ubd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

CO-CRYSTAL STRUCTURE OF HUMAN YY1 ZINC FINGER DOMAIN BOUND TO THE ADENO-ASSOCIATED VIRUS P5 INITIATOR ELEMENT

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

PROTEIN (YY1 ZINC FINGER DOMAIN)

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

1ubd__assembly_1__model_1

1ubd__assembly_1__model_1 | I(q)

1ubd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)