SAXSdb — 2er8

▼

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

Regulatory protein LEU3

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	5'-D(CPCPCPGPGPTPAPCPCPGPGPG)-3' × 2 ZINC ION × 4 water × 4	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 2 DNA 2	5'-D(CPCPCPGPGPTPAPCPCPGPGPG)-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	LEUR_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–72； UniProt 32–103 Author chain B； PDBConstruct 1–72； UniProt 32–103 Author chain C； PDBConstruct 1–72； UniProt 32–103 Author chain D； PDBConstruct 1–72； UniProt 32–103

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2er8
Deposition date deposition_date	2005-10-24
Structure title title	Crystal Structure of Leu3 DNA-binding domain complexed with a 12mer DNA duplex
Keywords keywords	Zn(2)Cys(6) Binuclear Cluster Motif, TRANSCRIPTION ACTIVATOR-DNA COMPLEX; TRANSCRIPTION ACTIVATOR/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2er8__assembly_1__model_1

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

Download this curve (.dat)

2er8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2er8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.70 Å
Rg (electron density)	21.87 Å
Total Rg	22.07 Å
Atom count	1512
Residues	159
Excluded volume	25275 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2er8__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2er8__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	5'-D(CPCPCPGPGPTPAPCPCPGPGPG)-3'
Molecular weight formula_weight	3664.4 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,F,G,H
Atom count atom_count	3032

CCCGGTACCGGG

Entity 2 Entity 2 polymer

Description description	Regulatory protein LEU3
Molecular weight formula_weight	8596.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

KRKFACVECRQQKSKCDAHERAPEPCTKCAKKNVPCILKRDFRRTYKRARNEAIEKRFKELTRTLTNLTSDE

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;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	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	33

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2er8A00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	240 — CD2-Gal4
Homologous superfamily homologous superfamily	10 — Zn(2)-C6 fungal-type DNA-binding domain

Domain ID domain_id	2er8B00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	240 — CD2-Gal4
Homologous superfamily homologous superfamily	10 — Zn(2)-C6 fungal-type DNA-binding domain

Domain ID domain_id	2er8C00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	240 — CD2-Gal4
Homologous superfamily homologous superfamily	10 — Zn(2)-C6 fungal-type DNA-binding domain

Domain ID domain_id	2er8D00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	240 — CD2-Gal4
Homologous superfamily homologous superfamily	10 — Zn(2)-C6 fungal-type DNA-binding domain

▶

Unit-cell length a length_a	107.500 Å
Unit-cell length b length_b	107.500 Å
Unit-cell length c length_c	218.900 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	48

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	45.530 Å
R factor r_factor	0.2370
R_work r_work	0.2370
R_free r_free	0.2650

Crystal Structure of Leu3 DNA-binding domain complexed with a 12mer DNA duplex

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

Regulatory protein LEU3

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

2er8__assembly_1__model_1

2er8__assembly_1__model_1 | I(q)

2er8__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Leu3 DNA-binding domain complexed with a 12mer DNA duplex

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

Regulatory protein LEU3

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

2er8__assembly_1__model_1

2er8__assembly_1__model_1 | I(q)

2er8__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)