SAXSdb — 2l5b

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

Activator of apoptosis harakiri

OrganismNot specified

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 61–91	Fragment：UNP Residues 61-91 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 3.2；323 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition：1.0-1.5 mM Hrk-TM, 200 mM D25 SDS, 5 mM D15 TCEP, 0.1 mM sodium azide, 35% v/v D3 methanol, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：1.0-1.5 mM Hrk-TM, 200 mM D25 SDS, 0.1 mM sodium azide, 5 mM D15 TCEP, 35% v/v D4 methanol, 100% D2O \| 100% D2O	Resolution not provided

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 2L5B	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2L58 Solution structure of the cytosolic fragment 22-53 of Bcl-2 member Harakiri Deposited 2010-10-28	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–53（32 aa） Fragment：UNP residues 22-53	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.8；303 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 1.0-1.5 mM Hrk-22_53, 0.1 mM sodium azide, 20 mM sodium phosphate, 35% v/v d3 TFE, 100% D2O \| 100% D2O NMR sample composition 1.0-1.5 mM Hrk-22_53, 0.1 mM sodium azide, 20 mM sodium phosphate, 35% v/v d2 TFE, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6XY4 Structural insight into sheep-pox virus mediated inhibition of apoptosis Deposited 2020-01-29	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 26–51（26 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Bis-Tris propane pH 6.5, 20% w/vPEG 3350	Resolution 2.05 Å R-free 0.234
7P0U ORF virus encoded Bcl-2 homolog ORFV125 in complex with Puma BH3 peptide Deposited 2021-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 26–51（26 aa） Chain U 26–51（26 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Bis-Tris propane pH 8.5, 20% PEG 3350	Resolution 1.99 Å R-free 0.274
7P0U ORF virus encoded Bcl-2 homolog ORFV125 in complex with Puma BH3 peptide Deposited 2021-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 26–51（26 aa） Chain G 26–51（26 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Bis-Tris propane pH 8.5, 20% PEG 3350	Resolution 1.99 Å R-free 0.274
9LGU Crystal structure of Bcl-xL in complex with stapled HRK peptide Deposited 2025-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 27–50（24 aa） Chain F 27–50（24 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5 and 25% w/v Polyethylene glycol 3,350 (w/v)	Resolution 2.97 Å R-free 0.303
9LGU Crystal structure of Bcl-xL in complex with stapled HRK peptide Deposited 2025-01-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 27–50（24 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5 and 25% w/v Polyethylene glycol 3,350 (w/v)	Resolution 2.97 Å R-free 0.303
9LGU Crystal structure of Bcl-xL in complex with stapled HRK peptide Deposited 2025-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 27–50（24 aa） Chain H 27–50（24 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5 and 25% w/v Polyethylene glycol 3,350 (w/v)	Resolution 2.97 Å R-free 0.303
9LGU Crystal structure of Bcl-xL in complex with stapled HRK peptide Deposited 2025-01-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 27–50（24 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5 and 25% w/v Polyethylene glycol 3,350 (w/v)	Resolution 2.97 Å R-free 0.303
9LGU Crystal structure of Bcl-xL in complex with stapled HRK peptide Deposited 2025-01-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 27–50（24 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5 and 25% w/v Polyethylene glycol 3,350 (w/v)	Resolution 2.97 Å R-free 0.303
9LGU Crystal structure of Bcl-xL in complex with stapled HRK peptide Deposited 2025-01-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 27–50（24 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5 and 25% w/v Polyethylene glycol 3,350 (w/v)	Resolution 2.97 Å R-free 0.303
9LGU Crystal structure of Bcl-xL in complex with stapled HRK peptide Deposited 2025-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 27–50（24 aa） Chain M 27–50（24 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5 and 25% w/v Polyethylene glycol 3,350 (w/v)	Resolution 2.97 Å R-free 0.303
9LGU Crystal structure of Bcl-xL in complex with stapled HRK peptide Deposited 2025-01-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 27–50（24 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5 and 25% w/v Polyethylene glycol 3,350 (w/v)	Resolution 2.97 Å R-free 0.303
9LGU Crystal structure of Bcl-xL in complex with stapled HRK peptide Deposited 2025-01-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 27–50（24 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5 and 25% w/v Polyethylene glycol 3,350 (w/v)	Resolution 2.97 Å R-free 0.303
9LI8 Crystal structure of Bcl-xL in complex with HRK BH3 peptide Deposited 2025-01-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 27–51（25 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5 and 25% w/v Polyethylene glycol 3350.	Resolution 2.32 Å R-free 0.264
9UGP Crystal structure of MCL-1 in complex with HRK BH3 Deposited 2025-04-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 27–51（25 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.1 M BIS-TRIS pH 6.5, 25%(w/v) polyethylene glycol monomethyl ether 2000	Resolution 1.39 Å R-free 0.197

6 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HRK_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–31； UniProt 61–91

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	2l5b
Deposition date deposition_date	2010-10-29
Structure title title	Solution structure of the transmembrane domain of Bcl-2 member Harakiri in micelles
Keywords keywords	Apoptosis, Bcl-2, BH3-only, Harakiri, transmembrane domain; APOPTOSIS
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.14 Å
Radius of gyration Rg (electron density) rg_electron	14.68 Å
Forward intensity I(0) i0	52367800.00
Molecular weight molecular_weight	66460.0 kDa
Excluded volume excluded_volume	85503 Å³
Envelope volume envelope_volume	11525 Å³
Hydration-shell volume shell_volume	6437 Å³
Envelope diameter envelope_diameter	59.8 Å
Shell Rg shell_rg	20.89 Å
Envelope Rg envelope_rg	19.03 Å
Shape Rg shape_rg	14.65 Å
Total Rg total_rg	14.99 Å
Total atoms total_atoms	9560
Residues n_residues	620
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	57.8 Å
Rg (real space) rg_real	14.73 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	5.2370e+07
I(0) uncertainty (real space) i0_real_error	8.0870e+05
Rg (reciprocal space) rg_reciprocal	14.69 Å
I(0) (reciprocal space) i0_reciprocal	52370000.0000
Solution quality estimate total_estimate	0.6123
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	5.1 Å
Skewness Skewness skewness	0.631
Kurtosis Kurtosis kurtosis	-0.439
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4531.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.001; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.001; Smooth: 0.952

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Description description	Activator of apoptosis harakiri
Molecular weight formula_weight	3321.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9560

fit	/app/data/saxs_computation/l5/2l5b/2l5b.fit
pddf	/app/data/pr_computation/l5/2l5b/2l5b.pr.out
profile	/app/data/saxs_computation/l5/2l5b/2l5b.dat

Solution structure of the transmembrane domain of Bcl-2 member Harakiri in micelles

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

Activator of apoptosis harakiri

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)