SAXSdb — 4yk9

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

Bcl-2-like protein 1

Mus musculus

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–196	Fragment：UNP RESIDUES 2-196	BH3BIM × 1 ACT ACETATE ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；287 K；0.1 M sodium acetate (pH 4.6), 0.01 M calcium chloride and 15% v/v 2-methyl-2,4-pentanediol	Resolution 1.70 Å R-free 0.228
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 2–196	Fragment：UNP RESIDUES 2-196	BH3BIM × 1 ACT ACETATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；287 K；0.1 M sodium acetate (pH 4.6), 0.01 M calcium chloride and 15% v/v 2-methyl-2,4-pentanediol	Resolution 1.70 Å R-free 0.228

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 4YK9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1PQ0 Crystal structure of mouse Bcl-xl Deposited 2003-06-17	Different construct 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 1–196（196 aa） Fragment：Bcl-xl	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；NH4SO4, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.243
1PQ1 Crystal structure of Bcl-xl/Bim Deposited 2003-06-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–196（196 aa） Fragment：BIM	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；NH4H2PO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.65 Å R-free 0.237
2BZW The crystal structure of BCL-XL in complex with full-length BAD Deposited 2005-08-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–211（211 aa） Fragment：BCL-2 HOMOLOGY DOMAIN, RESIDUES 1-211	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.248
3IHC Crystal structure of mouse Bcl-xl (wt) at pH 5.0 Deposited 2009-07-30	Different construct 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 1–196（196 aa） Fragment：UNP residues 1-196	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；1.6M Ammonium sulphate, Tri-Na citrate (pH 5.0), VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.85 Å R-free 0.242
3IHD Crystal structure of mouse Bcl-xl mutant (Y101A) at pH 5.0 Deposited 2009-07-30	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 1–196（196 aa） Fragment：UNP residues 1-196	Mutation：Y101A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；1.4M Ammonium Sulphate, Tri-Na citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.88 Å R-free 0.210
3IHE Crystal structure of mouse Bcl-xl mutant (F105A) at pH 6.0 Deposited 2009-07-30	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 1–196（196 aa） Fragment：UNP residues 1-196	Mutation：F105A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；1.7M Ammonium sulphate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.00 Å R-free 0.239
3IHF Crystal structure of mouse Bcl-xl mutant (R139A) at pH 5.0 Deposited 2009-07-30	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 1–196（196 aa） Fragment：UNP residues 1-196	Mutation：R139A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；1.45M Ammonium sulphate, Tri-Na citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.28 Å R-free 0.266
3IHF Crystal structure of mouse Bcl-xl mutant (R139A) at pH 5.0 Deposited 2009-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–196（196 aa） Fragment：UNP residues 1-196	Mutation：R139A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；1.45M Ammonium sulphate, Tri-Na citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.28 Å R-free 0.266
3IHF Crystal structure of mouse Bcl-xl mutant (R139A) at pH 5.0 Deposited 2009-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–196（196 aa） Fragment：UNP residues 1-196	Mutation：R139A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；1.45M Ammonium sulphate, Tri-Na citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.28 Å R-free 0.266
3IHF Crystal structure of mouse Bcl-xl mutant (R139A) at pH 5.0 Deposited 2009-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–196（196 aa） Fragment：UNP residues 1-196	Mutation：R139A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；1.45M Ammonium sulphate, Tri-Na citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.28 Å R-free 0.266
3IIG Crystal structure of mouse Bcl-xl mutant (F105A) at pH 5.0 Deposited 2009-08-01	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 1–196（196 aa） Fragment：UNP residues 1-196	Mutation：F105A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；1.6M Ammonium sulphate, 0.1M tri-Na citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.30 Å R-free 0.269
3IIH Crystal structure of mouse Bcl-xl (wt) at pH 6.0 Deposited 2009-08-01	Different construct 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 1–196（196 aa） Fragment：UNP residues 1-196	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；1.0M Ammonium sulphate, 0.4M Lithium sulphate, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.75 Å R-free 0.275
3ILB Crystal structure of mouse Bcl-xl mutant (R139A) at pH 6.0 Deposited 2009-08-07	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 1–196（196 aa） Fragment：UNP residues 1-196	Mutation：R139A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；1.2M Ammonium sulphate, 0.3M Lithium sulphate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.38 Å R-free 0.293
3ILB Crystal structure of mouse Bcl-xl mutant (R139A) at pH 6.0 Deposited 2009-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain N 1–196（196 aa） Fragment：UNP residues 1-196	Mutation：R139A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；1.2M Ammonium sulphate, 0.3M Lithium sulphate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.38 Å R-free 0.293
3ILC Crystal structure of mouse Bcl-xl mutant (Y101A) at pH 6.0 Deposited 2009-08-07	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 1–196（196 aa） Fragment：UNP residues 1-196	Mutation：Y101A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；1.6M Ammonium sulphate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.64 Å R-free 0.244
4YJ4 Crystal structure of Bcl-xL in complex with the BIM BH3 domain containing Ile155-to-Arg and Glu158-to-phosphoserine mutations Deposited 2015-03-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–196（196 aa）	Mutation：M83E, A84S	ACT ACETATE ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.8；293 K；0.1 M sodium acetate (pH 4.8), 3.0 M sodium chloride	Resolution 2.10 Å R-free 0.211
5C3G Crystal structure of Bcl-xl bound to BIM-MM Deposited 2015-06-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–26（26 aa） Fragment：UNP residues 1-26,UNP residues 83-209	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；12% Peg 1500, 0.1M Sodium Acetate pH 5.5, 2.5M NaCl, 1.5% MPD	Resolution 2.45 Å R-free 0.274
7WJH Crystal structure of Bcl-xL bound to the BH3 domain of human Pxt1 Deposited 2022-01-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–42（42 aa） Chain A 85–196（112 aa）	Not recorded	SO4 SULFATE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M ammonium sulfate and 30% (w/v) polyethylene glycol 8,000	Resolution 1.70 Å R-free 0.207
7Y99 Crystal Structure Analysis of cp2 bound BCLxl Deposited 2022-06-24	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 1–26（26 aa） Chain A 82–196（115 aa）	Not recorded	IQ8 N-(2-acetamidoethyl)-4-(4,5-dihydro-1,3-thiazol-2-yl)benzamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；Ammonium acetate, BIS-TRIS, MPD	Resolution 1.90 Å R-free 0.192

15 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	B2CL1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–195； UniProt 2–196 Author chain F； PDBConstruct 1–195； UniProt 2–196

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	4yk9
Deposition date deposition_date	2015-03-04
Structure title title	Complex structure of BCL-XL and mutated BIM BH3 domain
Keywords keywords	BCL-XL, BIM, BH3, complex, APOPTOSIS; 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	23.33 Å
Radius of gyration Rg (electron density) rg_electron	22.46 Å
Forward intensity I(0) i0	25731000.00
Molecular weight molecular_weight	38139.0 kDa
Excluded volume excluded_volume	47327 Å³
Envelope volume envelope_volume	55578 Å³
Hydration-shell volume shell_volume	21376 Å³
Envelope diameter envelope_diameter	76.8 Å
Shell Rg shell_rg	28.59 Å
Envelope Rg envelope_rg	22.58 Å
Shape Rg shape_rg	22.46 Å
Total Rg total_rg	23.22 Å
Total atoms total_atoms	2695
Residues n_residues	320
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	77.5 Å
Rg (real space) rg_real	23.40 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	2.5730e+07
I(0) uncertainty (real space) i0_real_error	3.3510e+05
Rg (reciprocal space) rg_reciprocal	23.39 Å
I(0) (reciprocal space) i0_reciprocal	25730000.0000
Solution quality estimate total_estimate	0.8697
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.450
Kurtosis Kurtosis kurtosis	-0.348
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	9047000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.969

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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	Bcl-2-like protein 1
Molecular weight formula_weight	21925.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	2824

SQSNRELVVDFLSYKLSQKGYSWSQFSDVEENRTEAPEETEAERETPSAINGNPSWHLADSPAVNGATGHSSSLDAREVIPMAAVKQALREAGDEFELRYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDKEMQVLVSRIASWMATYLNDHLEPWIQENGGWDTFVDLYG

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	BH3BIM
Molecular weight formula_weight	2669.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

XIWIAQELRSRGDSFNAYYAR

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	117

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4yk9A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	437 — Apoptosis Regulator Bcl-x
Homologous superfamily homologous superfamily	10 — Blc2-like

Domain ID domain_id	4yk9F00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	437 — Apoptosis Regulator Bcl-x
Homologous superfamily homologous superfamily	10 — Blc2-like

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8. Citations (2)

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Unit-cell length a length_a	81.738 Å
Unit-cell length b length_b	81.738 Å
Unit-cell length c length_c	42.568 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	6

Space group space_group	P 3
Space-group number int_tables_number	143
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	19.633 Å
R factor r_factor	0.1941
R_work r_work	0.1923
R_free r_free	0.2275

fit	/app/data/saxs_computation/yk/4yk9/4yk9.fit
pddf	/app/data/pr_computation/yk/4yk9/4yk9.pr.out
profile	/app/data/saxs_computation/yk/4yk9/4yk9.dat

Complex structure of BCL-XL and mutated BIM BH3 domain

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

Bcl-2-like protein 1

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

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)