SAXSdb — 4ayz

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

HEME-BINDING PROTEIN 2

HOMO SAPIENS

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–205 Chain B； UniProt 1–205	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.6；1.8 M NA/K PHOSPHATE BUFFER 5.6	Resolution 3.50 Å R-free 0.270

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 4AYZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3R85 Crystal structure of human SOUL BH3 domain in complex with Bcl-xL Deposited 2011-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 147–172（26 aa） Fragment：residues 147 to 172	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.2M sodium sulphate, 15% PEG 6000, 0.3M 1-butyl-3-methylimidazolium 2-(2-methoxyethoxy)ethyl sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.263
3R85 Crystal structure of human SOUL BH3 domain in complex with Bcl-xL Deposited 2011-03-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 147–172（26 aa） Fragment：residues 147 to 172	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.2M sodium sulphate, 15% PEG 6000, 0.3M 1-butyl-3-methylimidazolium 2-(2-methoxyethoxy)ethyl sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.263
3R85 Crystal structure of human SOUL BH3 domain in complex with Bcl-xL Deposited 2011-03-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 147–172（26 aa） Fragment：residues 147 to 172	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.2M sodium sulphate, 15% PEG 6000, 0.3M 1-butyl-3-methylimidazolium 2-(2-methoxyethoxy)ethyl sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.263
3R85 Crystal structure of human SOUL BH3 domain in complex with Bcl-xL Deposited 2011-03-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 147–172（26 aa） Fragment：residues 147 to 172	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.2M sodium sulphate, 15% PEG 6000, 0.3M 1-butyl-3-methylimidazolium 2-(2-methoxyethoxy)ethyl sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.263
3R8J Crystal structure of human SOUL protein (orthorhombic form) Deposited 2011-03-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–205（204 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；KH2PO4 0.8M, NaH2PO4 0.8M, HEPES 0.08M, 1-butyl-3-methylimidazolium chloride 0.2M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.197
3R8J Crystal structure of human SOUL protein (orthorhombic form) Deposited 2011-03-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–205（204 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；KH2PO4 0.8M, NaH2PO4 0.8M, HEPES 0.08M, 1-butyl-3-methylimidazolium chloride 0.2M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.197
3R8K Crystal structure of human SOUL protein (hexagonal form) Deposited 2011-03-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–205（204 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；2.0M ammonium sulphate, 0.1M Tris-HCl, 0.2M 1-butyl-3-methylimidazolium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.85 Å R-free 0.268
3R8K Crystal structure of human SOUL protein (hexagonal form) Deposited 2011-03-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–205（204 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；2.0M ammonium sulphate, 0.1M Tris-HCl, 0.2M 1-butyl-3-methylimidazolium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.85 Å R-free 0.268
3R8K Crystal structure of human SOUL protein (hexagonal form) Deposited 2011-03-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2–205（204 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；2.0M ammonium sulphate, 0.1M Tris-HCl, 0.2M 1-butyl-3-methylimidazolium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.85 Å R-free 0.268
3R8K Crystal structure of human SOUL protein (hexagonal form) Deposited 2011-03-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 2–205（204 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；2.0M ammonium sulphate, 0.1M Tris-HCl, 0.2M 1-butyl-3-methylimidazolium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.85 Å R-free 0.268
4B0Y Determination of X-ray Structure of human SOUL by Molecular Replacement Deposited 2012-07-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–205（205 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；2 M AMMONIUM SULPHATE, 0.1 M MES 6.5	Resolution 3.50 Å R-free 0.306
5GQQ Structure of ALG-2/HEBP2 Complex Deposited 2016-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 20–197（178 aa） Fragment：UNP RESIDUES 20-197 Chain B 20–197（178 aa） Fragment：UNP RESIDUES 20-197	Not recorded	CA CALCIUM ION × 6 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1 M Bis-Tris, 2 M NaCl, pH 5.5	Resolution 2.20 Å R-free 0.225

5 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HEBP2_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 4–208； UniProt 1–205 Author chain B； PDBConstruct 4–208； UniProt 1–205

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	4ayz
Deposition date deposition_date	2012-06-22
Structure title title	X-ray Structure of human SOUL
Keywords keywords	APOPTOSIS, HEME BINDING PROTEIN; APOPTOSIS
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	25.09 Å
Radius of gyration Rg (electron density) rg_electron	24.50 Å
Forward intensity I(0) i0	26817900.00
Molecular weight molecular_weight	38934.0 kDa
Excluded volume excluded_volume	48161 Å³
Envelope volume envelope_volume	60093 Å³
Hydration-shell volume shell_volume	21734 Å³
Envelope diameter envelope_diameter	89.4 Å
Shell Rg shell_rg	30.03 Å
Envelope Rg envelope_rg	24.76 Å
Shape Rg shape_rg	24.46 Å
Total Rg total_rg	25.27 Å
Total atoms total_atoms	2729
Residues n_residues	356
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	87.0 Å
Rg (real space) rg_real	25.22 Å
Rg uncertainty (real space) rg_real_error	0.98 Å
I(0) (real space) i0_real	2.6820e+07
I(0) uncertainty (real space) i0_real_error	4.1640e+05
Rg (reciprocal space) rg_reciprocal	25.18 Å
I(0) (reciprocal space) i0_reciprocal	26820000.0000
Solution quality estimate total_estimate	0.8440
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.486
Kurtosis Kurtosis kurtosis	-0.307
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9077000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.753; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.725; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	HEME-BINDING PROTEIN 2
Molecular weight formula_weight	23396.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2729

AGHMAEPLQPDPGAAEDAAAQAVETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFSESTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQKNEPTKENE

来源 Source

来源生物 organism	HOMO SAPIENS
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	HEME-BINDING PROTEIN 2
Molecular weight formula_weight	23396.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AGHMAEPLQPDPGAAEDAAAQAVETPGWKAPEDAGPQPGSYEIRHYGPAKWVSTSVESMDWDSAIQTGFTKLNSYIQGKNEKEMKIKMTAPVTSYVEPGSGPFESSTITISLYIPSEQQFDPPRPLESDVFIEDRAEMTVFVRSFDGFSSAQKNQEQLLTLASILREDGKVFDEKVYYTAGYNSPVKLLNRNNEVWLIQKNEPTKENE

来源 Source

来源生物 organism	HOMO SAPIENS
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4ayzA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	80 — Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A
Homologous superfamily homologous superfamily	10 — Regulatory factor, effector binding domain

Domain ID domain_id	4ayzB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	80 — Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A
Homologous superfamily homologous superfamily	10 — Regulatory factor, effector binding domain

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8. Citations (1)

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Unit-cell length a length_a	146.440 Å
Unit-cell length b length_b	146.440 Å
Unit-cell length c length_c	133.040 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 62 2 2
Space-group number int_tables_number	180
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2380
R_work r_work	0.2344
R_free r_free	0.2704

fit	/app/data/saxs_computation/ay/4ayz/4ayz.fit
pddf	/app/data/pr_computation/ay/4ayz/4ayz.pr.out
profile	/app/data/saxs_computation/ay/4ayz/4ayz.dat

X-ray Structure of human SOUL

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

HEME-BINDING PROTEIN 2

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)