SAXSdb — 1d66

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

PROTEIN (GAL4)

Saccharomyces cerevisiae

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 1–65 Chain B； UniProt 1–65	Not recorded	;DNA (5'-D(CPCPGPGPAPGPGPAPCPAPGPTPCPCPTPCPC PGPG)-3') ; × 1 ;DNA (5'-D(CPCPGPGPAPGPGPAPCPTPGPTPCPCPTPCPC PGPG)-3') ; × 1 CD CADMIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；pH 6.80, VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å

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 1D66	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AW6 GAL4 (CD), NMR, 24 STRUCTURES Deposited 1997-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–43（43 aa） Fragment：DNA-BINDING DOMAIN	Not recorded	CD CADMIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 7.2；298 K	Resolution not provided
1HBW Solution nmr structure of the dimerization domain of the yeast transcriptional activator Gal4 (residues 50-106) Deposited 2001-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 50–106（57 aa） Fragment：DIMERIZATION DOMAIN RESIDUES 50-106 Chain B 50–106（57 aa） Fragment：DIMERIZATION DOMAIN RESIDUES 50-106	Mutation：YES Mutation：YES	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；308 K；Ionic strength (raw mmCIF value) 50 MM SODIUM PHOSPHATE	Resolution not provided
3BTS Crystal structure of a ternary complex of the transcriptional repressor Gal80p (Gal80S0 [G301R]) and the acidic activation domain of Gal4p (aa 854-874) from Saccharomyces cerevisiae with NAD Deposited 2007-12-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 854–874（21 aa） Fragment：S. cerevisiae Gal4p peptide; UNP residues 854-874 Chain F 854–874（21 aa） Fragment：S. cerevisiae Gal4p peptide; UNP residues 854-874	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；20% PEG 3350, 0.15M Sodium fluoride, followed by soaking in NAD to a final concentration of 5mM, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.70 Å R-free 0.232
3COQ Structural Basis for Dimerization in DNA Recognition by Gal4 Deposited 2008-03-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 8–96（89 aa） Fragment：DNA binding domain with complete dimerization domain Chain B 8–96（89 aa） Fragment：DNA binding domain with complete dimerization domain	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；298 K；40mM Mg(OAc)2, 25mM sodium phosphate, 5% PEG400, 5% MPD, pH 5.5, VAPOR DIFFUSION, temperature 298K	Resolution 2.40 Å R-free 0.269
7UIK Mediator-PIC Early (Tail A + Upstream DNA & Activator) Deposited 2022-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain T 1–147（147 aa） Chain U 1–147（147 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.70 Å
7UIO Mediator-PIC Early (Composite Model) Deposited 2022-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric	Chain GA 1–147（147 aa） Chain GB 1–147（147 aa）	Not recorded	ZN ZINC ION × 4 THR THREONINE × 1 ALA ALANINE × 1 ASP ASPARTIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GAL4_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–65； UniProt 1–65 Author chain B； PDBConstruct 1–65； UniProt 1–65

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	1d66
Deposition date deposition_date	1992-03-06
Structure title title	DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX
Keywords keywords	PROTEIN-DNA COMPLEX, DOUBLE HELIX, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
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	23.13 Å
Radius of gyration Rg (electron density) rg_electron	23.67 Å
Forward intensity I(0) i0	20310800.00
Molecular weight molecular_weight	25587.0 kDa
Excluded volume excluded_volume	28162 Å³
Envelope volume envelope_volume	39788 Å³
Hydration-shell volume shell_volume	15889 Å³
Envelope diameter envelope_diameter	86.9 Å
Shell Rg shell_rg	27.64 Å
Envelope Rg envelope_rg	23.48 Å
Shape Rg shape_rg	23.56 Å
Total Rg total_rg	24.32 Å
Total atoms total_atoms	1711
Residues n_residues	152
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	84.2 Å
Rg (real space) rg_real	23.34 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	2.0310e+07
I(0) uncertainty (real space) i0_real_error	2.7930e+05
Rg (reciprocal space) rg_reciprocal	23.29 Å
I(0) (reciprocal space) i0_reciprocal	20310000.0000
Solution quality estimate total_estimate	0.8350
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.3 Å
Skewness Skewness skewness	0.488
Kurtosis Kurtosis kurtosis	-0.297
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	751000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.756; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.584; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(CPCPGPGPAPGPGPAPCPAPGPTPCPCPTPCPC PGP*G)-3') ;
Molecular weight formula_weight	5831.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D
Atom count atom_count	1762

CCGGAGGACAGTCCTCCGG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(CPCPGPGPAPGPGPAPCPTPGPTPCPCPTPCPC PGP*G)-3') ;
Molecular weight formula_weight	5822.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

CCGGAGGACTGTCCTCCGG

Entity 3 Entity 3 polymer

Description description	PROTEIN (GAL4)
Molecular weight formula_weight	7816.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MKLLSSIEQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTRAHLTEVESRLERLEF

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 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	51

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1d66a1
Class class	g — Small proteins
Fold Fold fold	g.38 — Zn2/Cys6 DNA-binding domain
Superfamily Superfamily superfamily	g.38.1 — Zn2/Cys6 DNA-binding domain
Family Family family	g.38.1.1 — Zn2/Cys6 DNA-binding domain

Domain ID domain_id	d1d66a2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.3 — Leucine zipper domain
Family Family family	h.1.3.1 — Leucine zipper domain

Domain ID domain_id	d1d66b1
Class class	g — Small proteins
Fold Fold fold	g.38 — Zn2/Cys6 DNA-binding domain
Superfamily Superfamily superfamily	g.38.1 — Zn2/Cys6 DNA-binding domain
Family Family family	g.38.1.1 — Zn2/Cys6 DNA-binding domain

Domain ID domain_id	d1d66b2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.3 — Leucine zipper domain
Family Family family	h.1.3.1 — Leucine zipper domain

CATH v4.4 (3 domains)

Domain ID domain_id	1d66A00
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	1d66B01
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	1d66B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	640 — Single helix bin

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8. Citations (1)

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Unit-cell length a length_a	80.850 Å
Unit-cell length b length_b	80.850 Å
Unit-cell length c length_c	73.700 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2300
R_work r_work	0.2300
R_free r_free	—

fit	/app/data/saxs_computation/d6/1d66/1d66.fit
pddf	/app/data/pr_computation/d6/1d66/1d66.pr.out
profile	/app/data/saxs_computation/d6/1d66/1d66.dat

DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX

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

PROTEIN (GAL4)

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)