SAXSdb — 1llm

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

chimera of Zif23-GCN4

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2 DNA 2	5'-D(TPCPCPCPAPCPGPCPGPTPGPGP*G)-3' × 2 ZINC ION × 4 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GCN4_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 60–88； UniProt 253–281 Author chain D； PDBConstruct 60–88； UniProt 253–281

chimera of Zif23-GCN4

Saccharomyces cerevisiae

UniProt P08046

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2 DNA 2	5'-D(TPCPCPCPAPCPGPCPGPTPGPGP*G)-3' × 2 ZINC ION × 4 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EGR1_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–50； UniProt 364–412 Author chain D； PDBConstruct 2–50； UniProt 364–412

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	1llm
Deposition date deposition_date	2002-04-29
Structure title title	Crystal Structure of a Zif23-GCN4 Chimera Bound to DNA
Keywords keywords	Dimerization, DNA recognition, leucine zipper, structure-based design, zinc fingers, 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.

1llm__assembly_1__model_1

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

Download this curve (.dat)

1llm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1llm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.10 Å
Rg (electron density)	23.69 Å
Total Rg	24.02 Å
Atom count	1967
Residues	198
Excluded volume	33232 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1llm__assembly_1__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	5'-D(TPCPCPCPAPCPGPCPGPTPGPGP*G)-3'
Molecular weight formula_weight	3968.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A,B
Atom count atom_count	2323

TCCCACGCGTGGG

Entity 2 Entity 2 polymer

Description description	chimera of Zif23-GCN4
Molecular weight formula_weight	10553.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRHRDIQHILPILEDKVEELLSKNYHLENEVARLKKLVGER

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;house mouse, baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	312

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1llmc1
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	d1llmc2
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	d1llmc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1llmd1
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	d1llmd2
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	1llmC01
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	1llmC02
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	1llmD01
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	1llmD02
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	87.398 Å
Unit-cell length b length_b	87.398 Å
Unit-cell length c length_c	118.693 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	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2160
R_free r_free	0.2340

Crystal Structure of a Zif23-GCN4 Chimera Bound to DNA

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

chimera of Zif23-GCN4

State in the Current Structure

Other States of the Same Protein in the Database

chimera of Zif23-GCN4

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

1llm__assembly_1__model_1

1llm__assembly_1__model_1 | I(q)

1llm__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (2)

Crystal Structure of a Zif23-GCN4 Chimera Bound to DNA

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

chimera of Zif23-GCN4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

chimera of Zif23-GCN4

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

1llm__assembly_1__model_1

1llm__assembly_1__model_1 | I(q)

1llm__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (2)