SAXSdb — 7p0s

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

Apoptosis inhibitor

Orf virus

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 1–143 Chain B； UniProt 1–143	Not recorded	Bcl-2-binding component 3, isoforms 1/2 × 2 （Q9BXH1）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Magnesium acetate, 25% PEG 3350	Resolution 2.50 Å R-free 0.286

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 7P0S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7ADS Orf virus Apoptosis inhibitor ORFV125 Deposited 2020-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–143（143 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 14 NA SODIUM ION × 10 CL CHLORIDE ION × 4 MG MAGNESIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2M Sodium citrate tribasic dehydrate 0.02M magnesium chloride 0.1M Bis tris propane 20% PEG 3350	Resolution 2.22 Å R-free 0.260
7ADT Orf virus Apoptosis inhibitor ORFV125 Deposited 2020-09-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–143（143 aa） Chain B 1–143（143 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 7 GOL GLYCEROL × 2 MG MAGNESIUM ION × 41	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2 M Magnesium chloride hexahydrate, 0.1 M Bis-Tris pH 5.5, 25% PEG 3350	Resolution 2.21 Å R-free 0.259
7P0U ORF virus encoded Bcl-2 homolog ORFV125 in complex with Puma BH3 peptide Deposited 2021-06-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–143（143 aa） Chain D 1–143（143 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–143（143 aa） Chain F 1–143（143 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

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0R8HV90_ORFV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–148； UniProt 1–143 Author chain B； PDBConstruct 6–148； UniProt 1–143

Bcl-2-binding component 3, isoforms 1/2

OrganismNot specified

UniProt Q9BXH1

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 C； UniProt 130–155 Chain U； UniProt 130–155	Not recorded	Apoptosis inhibitor × 2 （A0A0R8HV90）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Magnesium acetate, 25% PEG 3350	Resolution 2.50 Å R-free 0.286

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 7P0S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2M04 Solution structure of BCL-xL in complex with PUMA BH3 peptide Deposited 2012-10-19	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 130–154（25 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298.1 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N; U-95% 2H; Ile,Leu,Val C1H3] BCL-xL, 0.9 mM PUMA BH3, 92% H2O/8% D2O \| 92% H2O/8% D2O NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N] BCL-xL, 0.9 mM PUMA BH3, 92% H2O/8% D2O \| 92% H2O/8% D2O	Resolution not provided
4HNJ Crystallographic structure of BCL-xL domain-swapped dimer in complex with PUMA BH3 peptide at 2.9A resolution Deposited 2012-10-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 130–154（25 aa） Fragment：BH3 domain peptide	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0.2 M CaCl2, 0.1 M NaOAc, 20% V/V isopropanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.90 Å R-free 0.254
5UUL Human Bfl-1 in complex with PUMA BH3 Deposited 2017-02-17	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 B 132–154（23 aa） Fragment：UNP residues 132-154	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；1.8 M ammonium sulfate, 0.1 M MES pH 7.0	Resolution 1.33 Å R-free 0.155
6QFM Structure of human Mcl-1 in complex with PUMA BH3 peptide Deposited 2019-01-10	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 B 127–149（23 aa）	Not recorded	ZN ZINC ION × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；100 mM imidazole buffer pH 7.0, 50 mM zinc acetate and 20-25% polyethylene glycol (PEG) 3350	Resolution 2.00 Å R-free 0.261
6QG8 Structure of human Bcl-2 in complex with PUMA BH3 peptide Deposited 2019-01-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 127–149（23 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；284 K；from 0.2M MgCl2, 25% PegMME 2k, 0.1M Na Acetate buffer pH 5.5	Resolution 1.90 Å R-free 0.216
6TQP Structural insight into tanapoxvirus mediated inhibition of apoptosis Deposited 2019-12-17	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 B 130–155（26 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M Potassium thiocyanate, 30% PEG 2000MME	Resolution 1.85 Å R-free 0.218
7DVD The crystal structure of p53 DNA binding domain and PUMA complex Deposited 2021-01-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 136–150（15 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.1 M Tris (pH 7.0) 20% (w/w) PEG-200 MME	Resolution 2.59 Å R-free 0.318
7P9W Epstein-Barr virus encoded apoptosis regulator BHRF1 in complex with Puma BH3 Deposited 2021-07-28	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 B 130–155（26 aa）	Not recorded	PO4 PHOSPHATE ION × 3 EDO 1,2-ETHANEDIOL × 6 NH4 AMMONIUM ION × 1 PDO 1,3-PROPANDIOL × 2 MG MAGNESIUM ION × 5 CL CHLORIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M Ammonium phosphate monobasic	Resolution 2.00 Å R-free 0.257
7QTX Kaposi sarcoma associated herpes virus (KSHV) encoded apoptosis inhibitor, KsBcl-2 in complex with Puma BH3 Deposited 2022-01-17	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 B 130–155（26 aa）	Not recorded	BR BROMIDE ION × 3 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M sodium bromide, 0.1 M Bis-tris propane pH 6.5, 20% PEG 3350	Resolution 2.12 Å R-free 0.257

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BBC3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–26； UniProt 130–155 Author chain U； 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	7p0s
Deposition date deposition_date	2021-06-30
Structure title title	ORF virus encoded Bcl-2 homolog ORFV125 in complex with Puma BH3 peptide
Keywords keywords	ORF virus, Bcl-2, 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	22.37 Å
Radius of gyration Rg (electron density) rg_electron	21.12 Å
Forward intensity I(0) i0	23436300.00
Molecular weight molecular_weight	35289.0 kDa
Excluded volume excluded_volume	43578 Å³
Envelope volume envelope_volume	53237 Å³
Hydration-shell volume shell_volume	21387 Å³
Envelope diameter envelope_diameter	77.2 Å
Shell Rg shell_rg	27.42 Å
Envelope Rg envelope_rg	21.44 Å
Shape Rg shape_rg	21.14 Å
Total Rg total_rg	21.88 Å
Total atoms total_atoms	4921
Residues n_residues	316
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	75.8 Å
Rg (real space) rg_real	22.36 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	2.3440e+07
I(0) uncertainty (real space) i0_real_error	2.9720e+05
Rg (reciprocal space) rg_reciprocal	22.36 Å
I(0) (reciprocal space) i0_reciprocal	23440000.0000
Solution quality estimate total_estimate	0.8764
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.347
Kurtosis Kurtosis kurtosis	-0.408
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7684000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Apoptosis inhibitor
Molecular weight formula_weight	16160.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4946

GPLGSMANRDDIDASAVMAAYLAREYAEAVEEQLTPRERDALEALRVSGEEVRSPLLQELSNAGEHRANPENSHIPAALVSALLEAPTSPGRMVTAVELCAQMGRLWTRGRQLVDFMRLVYVLLDRLPPTADEDLGAWLQAVARVHGT

来源 Source

来源生物 organism	Orf virus
通用名 common_name	ORFV
NCBI Class编号 ncbi_taxonomy_id	10258
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Bcl-2-binding component 3, isoforms 1/2
Molecular weight formula_weight	3210.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

EEQWAREIGAQLRRMADDLNAQYERR

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	25

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8. Citations (1)

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Unit-cell length a length_a	49.033 Å
Unit-cell length b length_b	69.564 Å
Unit-cell length c length_c	92.117 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.503 Å
Low-resolution limit resolution_low	43.283 Å
R factor r_factor	0.2468
R_work r_work	0.2447
R_free r_free	0.2858

fit	/app/data/saxs_computation/p0/7p0s/7p0s.fit
pddf	/app/data/pr_computation/p0/7p0s/7p0s.pr.out
profile	/app/data/saxs_computation/p0/7p0s/7p0s.dat

ORF virus encoded Bcl-2 homolog ORFV125 in complex with Puma BH3 peptide

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

Apoptosis inhibitor

State in the Current Structure

Other States of the Same Protein in the Database

Bcl-2-binding component 3, isoforms 1/2

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)