SAXSdb — 2hap

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

PROTEIN (HEME ACTIVATOR PROTEIN)

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	;DNA (5'-D(APCPGPCPTPAPTPTPAPTPCPGPCPTPAPTPTPAPGPT)-3') ; × 1 ;DNA (5'-D(APCPTPAPAPTPAPGPCPGPAPTPAPAPTPAPGPCPGPT)-3') ; × 1 ZINC ION × 5 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CYP1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–81； UniProt 55–135 Author chain D； PDBConstruct 1–81； UniProt 55–135

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	2hap
Deposition date deposition_date	1998-09-17
Structure title title	STRUCTURE OF A HAP1-18/DNA COMPLEX REVEALS THAT PROTEIN/DNA INTERACTIONS CAN HAVE DIRECT ALLOSTERIC EFFECTS ON TRANSCRIPTIONAL ACTIVATION
Keywords keywords	COMPLEX TRANSCRIPTION FACTOR-DNA, ASYMMETRY, TRANSCRIPTIONAL ACTIVATION, HYPERACTIVE MUTANT, GENE REGULATION-DNA COMPLEX; GENE REGULATION/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.

2hap__assembly_1__model_1

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

Download this curve (.dat)

2hap__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hap__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.22 Å
Rg (electron density)	23.11 Å
Total Rg	23.61 Å
Atom count	2074
Residues	191
Excluded volume	34587 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hap__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 (5)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(APCPGPCPTPAPTPTPAPTPCPGPCPTPAPTPTPAPGPT)-3') ;
Molecular weight formula_weight	6099.0 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	2148

ACGCTATTATCGCTATTAGT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APCPTPAPAPTPAPGPCPGPAPTPAPAPTPAPGPCPGPT)-3') ;
Molecular weight formula_weight	6166.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

ACTAATAGCGATAATAGCGT

Entity 3 Entity 3 polymer

Description description	PROTEIN (HEME ACTIVATOR PROTEIN)
Molecular weight formula_weight	9696.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

RKRNRIPLRCTICRKRKVKCDKLRPHCQQCTKTGVAHLCHYMEQTWAEEAEKELLKDNELKKLRERVKSLEKTLSKVHSSP

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 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	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	74

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2hapc1
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	d2hapc2
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	d2hapd1
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	d2hapd2
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 (4 domains)

Domain ID domain_id	2hapC01
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	2hapC02
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	170 —

Domain ID domain_id	2hapD01
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	2hapD02
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	170 —

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Unit-cell length a length_a	92.500 Å
Unit-cell length b length_b	92.500 Å
Unit-cell length c length_c	86.500 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2480
R_work r_work	0.2480
R_free r_free	0.3020

STRUCTURE OF A HAP1-18/DNA COMPLEX REVEALS THAT PROTEIN/DNA INTERACTIONS CAN HAVE DIRECT ALLOSTERIC EFFECTS ON TRANSCRIPTIONAL ACTIVATION

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

PROTEIN (HEME ACTIVATOR PROTEIN)

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

2hap__assembly_1__model_1

2hap__assembly_1__model_1 | I(q)

2hap__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 (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)

STRUCTURE OF A HAP1-18/DNA COMPLEX REVEALS THAT PROTEIN/DNA INTERACTIONS CAN HAVE DIRECT ALLOSTERIC EFFECTS ON TRANSCRIPTIONAL ACTIVATION

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

PROTEIN (HEME ACTIVATOR PROTEIN)

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

2hap__assembly_1__model_1

2hap__assembly_1__model_1 | I(q)

2hap__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 (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)