SAXSdb — 2vof

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

BCL-2-RELATED PROTEIN A1

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–152 Chain C； UniProt 1–152	Fragment：RESIDUES 1-152 Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	BCL-2-BINDING COMPONENT 3 × 2 （Q99ML1） CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：0.1 M CITRIC ACID.KOH (PH 4.35), 15% PEG 20,000, 0.4 M LICL, 20% GLYCEROL	Resolution 1.80 Å R-free 0.210
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–152	Fragment：RESIDUES 1-152 Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	BCL-2-BINDING COMPONENT 3 × 1 （Q99ML1） CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：0.1 M CITRIC ACID.KOH (PH 4.35), 15% PEG 20,000, 0.4 M LICL, 20% GLYCEROL	Resolution 1.80 Å R-free 0.210
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–152	Fragment：RESIDUES 1-152 Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	BCL-2-BINDING COMPONENT 3 × 1 （Q99ML1） CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：0.1 M CITRIC ACID.KOH (PH 4.35), 15% PEG 20,000, 0.4 M LICL, 20% GLYCEROL	Resolution 1.80 Å R-free 0.210

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 2VOF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2VOG Structure of mouse A1 bound to the Bmf BH3-domain Deposited 2008-02-17	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–152（152 aa） Fragment：RESIDUES 1-152	Mutation：YES	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 18% PEG 2000, 0.88 M LICL, 0.1 M CITRIC ACID, KOH (PH 4.35)	Resolution 1.90 Å R-free 0.231
2VOH Structure of mouse A1 bound to the Bak BH3-domain Deposited 2008-02-17	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 1–152（152 aa） Fragment：RESIDUES 1-152	Mutation：YES	CIT CITRIC ACID × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M SODIUM CITRATE (PH 5.6), 0.3 M (NH4)2SO4, 0.6 M LI2SO4	Resolution 1.90 Å R-free 0.229
2VOI Structure of mouse A1 bound to the Bid BH3-domain Deposited 2008-02-17	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–152（152 aa） Fragment：RESIDUES 1-152	Mutation：YES	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M CITRIC ACID, KOH (PH 4.2), 18% PEG 2000, 0.4 M LICL	Resolution 2.10 Å R-free 0.242

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	B2LA1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–157； UniProt 1–152 Author chain C； PDBConstruct 6–157； UniProt 1–152

BCL-2-BINDING COMPONENT 3

MUS MUSCULUS

UniProt Q99ML1

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 130–155 Chain D； UniProt 130–155	Fragment：BH3-DOMAIN, RESIDUES 130-155 Mutation：YES	BCL-2-RELATED PROTEIN A1 × 2 （Q07440） CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：0.1 M CITRIC ACID.KOH (PH 4.35), 15% PEG 20,000, 0.4 M LICL, 20% GLYCEROL	Resolution 1.80 Å R-free 0.210
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 130–155	Fragment：BH3-DOMAIN, RESIDUES 130-155 Mutation：YES	BCL-2-RELATED PROTEIN A1 × 1 （Q07440） CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：0.1 M CITRIC ACID.KOH (PH 4.35), 15% PEG 20,000, 0.4 M LICL, 20% GLYCEROL	Resolution 1.80 Å R-free 0.210
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 130–155	Fragment：BH3-DOMAIN, RESIDUES 130-155 Mutation：YES	BCL-2-RELATED PROTEIN A1 × 1 （Q07440） CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：0.1 M CITRIC ACID.KOH (PH 4.35), 15% PEG 20,000, 0.4 M LICL, 20% GLYCEROL	Resolution 1.80 Å R-free 0.210

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 2VOF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ROC Solution structure of Mcl-1 Complexed with Puma Deposited 2008-03-17	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 130–155（26 aa） Fragment：BH3 domain, residues 130-155	Mutation：M144I	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 120 mM；Pressure ambient NMR sample composition 0.5mM [U-100% 13C; U-100% 15N] Mcl-1; 0.5mM Puma; 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5mM Mcl-1; 0.5mM [U-100% 13C; U-100% 15N] Puma; 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BBC3_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–26； UniProt 130–155 Author chain D； PDBConstruct 1–26； UniProt 130–155

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	2vof
Deposition date deposition_date	2008-02-17
Structure title title	Structure of mouse A1 bound to the Puma BH3-domain
Keywords keywords	BH3, BCL-2, APOPTOSIS, PRO-SURVIVAL, MITOCHONDRION, PROTEIN-PROTEIN COMPLEX; 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	23.29 Å
Radius of gyration Rg (electron density) rg_electron	22.39 Å
Forward intensity I(0) i0	25825800.00
Molecular weight molecular_weight	38845.0 kDa
Excluded volume excluded_volume	48374 Å³
Envelope volume envelope_volume	56472 Å³
Hydration-shell volume shell_volume	21557 Å³
Envelope diameter envelope_diameter	88.6 Å
Shell Rg shell_rg	28.50 Å
Envelope Rg envelope_rg	22.84 Å
Shape Rg shape_rg	22.28 Å
Total Rg total_rg	23.46 Å
Total atoms total_atoms	2717
Residues n_residues	331
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	84.8 Å
Rg (real space) rg_real	23.35 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	2.5830e+07
I(0) uncertainty (real space) i0_real_error	3.4970e+05
Rg (reciprocal space) rg_reciprocal	23.34 Å
I(0) (reciprocal space) i0_reciprocal	25830000.0000
Solution quality estimate total_estimate	0.8275
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	0.430
Kurtosis Kurtosis kurtosis	-0.332
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8481000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.641; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.838; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	BCL-2-RELATED PROTEIN A1
Molecular weight formula_weight	18110.0 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2900

GPLGSMAESELMHIHSLAEHYLQYVLQVPAFESAPSQACRVLQRVAFSVQKEVEKNLKSYLDDFHVESIDTARIIFNQVMEKEFEDGIINWGRIVTIFAFGGVLLKKLKQEQIALDVSAYKQVSSFVAEFIMNNTGEWIRQNGGWEDGFIKKFEPKS

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	BCL-2-BINDING COMPONENT 3
Molecular weight formula_weight	3193.5 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

EEEWAREIGAQLRRIADDLNAQYERR

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 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2vofa1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.1 — Toxins' membrane translocation domains
Superfamily Superfamily superfamily	f.1.4 — Bcl-2 inhibitors of programmed cell death
Family Family family	f.1.4.0 — automated matches

Domain ID domain_id	d2vofa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2vofc1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.1 — Toxins' membrane translocation domains
Superfamily Superfamily superfamily	f.1.4 — Bcl-2 inhibitors of programmed cell death
Family Family family	f.1.4.0 — automated matches

Domain ID domain_id	d2vofc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	2vofA00
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	2vofC00
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 (1)

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Unit-cell length a length_a	49.640 Å
Unit-cell length b length_b	60.683 Å
Unit-cell length c length_c	59.986 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	43.980 Å
R factor r_factor	0.1840
R_work r_work	0.1830
R_free r_free	0.2100

fit	/app/data/saxs_computation/vo/2vof/2vof.fit
pddf	/app/data/pr_computation/vo/2vof/2vof.pr.out
profile	/app/data/saxs_computation/vo/2vof/2vof.dat

Structure of mouse A1 bound to the Puma BH3-domain

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

BCL-2-RELATED PROTEIN A1

State in the Current Structure

Other States of the Same Protein in the Database

BCL-2-BINDING COMPONENT 3

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)