SAXSdb — 4cim

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

BCL-2-LIKE 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 B； UniProt 1–163 Chain Q； UniProt 38–58	Mutation：YES Fragment：RESIDUES 38-58 Mutation：YES	EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；1 M TRISODIUM CITRATE 0.1 M IMIDAZOLE, PH 8.0	Resolution 1.50 Å R-free 0.210
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–163 Chain P； UniProt 38–58	Mutation：YES Fragment：RESIDUES 38-58 Mutation：YES	EDO 1,2-ETHANEDIOL × 9	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；1 M TRISODIUM CITRATE 0.1 M IMIDAZOLE, PH 8.0	Resolution 1.50 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 4CIM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1MK3 SOLUTION STRUCTURE OF HUMAN BCL-W PROTEIN Deposited 2002-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–171（170 aa）	Mutation：P116V	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.3；298 K；Ionic strength (raw mmCIF value) 10 mM NaCl；Pressure 1 NMR sample composition 1.4 mM Bcl-w protein U-15N,13C, 20 mM phosphate buffer \| 90% H2O/10% D2O NMR sample composition 1.3 mM Bcl-w protein U-15N, 20 mM phosphate buffer \| 90% H2O/10% D2O NMR sample composition 0.5 mM Bcl-w protein U-15N, 6 MG/ML PF1-PHAGE \| 90% H2O/10% D2O	Resolution not provided
1O0L THE STRUCTURE OF BCL-W REVEALS A ROLE FOR THE C-TERMINAL RESIDUES IN MODULATING BIOLOGICAL ACTIVITY Deposited 2003-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–183（183 aa）	Mutation：A128E	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；303.15 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR measurement conditions pH 6.7；303.15 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR measurement conditions pH 6.7；303.15 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1 mM Bcl-w \| 50mM Sodium Phosphate, 70mM NaCl, 2mM TCEP, 95% H2O, 5% D2O NMR sample composition 1 mM, U-15N Bcl-w \| 50mM Sodium Phosphate, 70mM NaCl, 2mM TCEP, 95% H2O, 5% D2O NMR sample composition 1 mM, U-13C, 15N, Bcl-w \| 50mM Sodium Phosphate, 70mM NaCl, 2mM TCEP, 95% H2O, 5% D2O	Resolution not provided
1ZY3 Structural model of complex of Bcl-w protein with Bid BH3-peptide Deposited 2005-06-09	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 × 2 PDB declaration: dimeric	Chain A 2–171（170 aa） Fragment：residues 2-171	Mutation：P116V	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 10 mM NaCl；Pressure 1 NMR sample composition 0.7 mM Bcl-w U-15N,13C, 0.7 mM Bid BH3-peptide, 20 mM phosphate buffer, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7 mM Bcl-w U-15N, 0.7 mM Bid BH3-peptide, 20 mM phosphate buffer, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7 mM Bid BH3-peptide U-15N, 0.7 mM Bcl-w, 20 mM phosphate buffer, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2Y6W Structure of a Bcl-w dimer Deposited 2011-01-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–164（164 aa） Fragment：C-TERMINAL TRUNCATION, RESIDUES 1-164 Chain B 1–164（164 aa） Fragment：C-TERMINAL TRUNCATION, RESIDUES 1-164	Mutation：YES Mutation：YES	PEG DI(HYDROXYETHYL)ETHER × 5 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；5% (W/V) PEG 3000, 40% (W/V) PEG 400, 0.1M MES PH 6.5.	Resolution 2.00 Å R-free 0.244

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

View Construct and Data Evidence

UniProt name	B2CL2_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–163； UniProt 1–163 Author chain B； PDBConstruct 1–163； UniProt 1–163 Author chain P； PDBConstruct 1–21； UniProt 38–58 Author chain Q； PDBConstruct 1–21； UniProt 38–58

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	4cim
Deposition date deposition_date	2013-12-12
Structure title title	Complex of a Bcl-w BH3 mutant with a BH3 domain
Keywords keywords	APOPTOSIS, CELL DEATH; 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	22.57 Å
Radius of gyration Rg (electron density) rg_electron	21.67 Å
Forward intensity I(0) i0	24022400.00
Molecular weight molecular_weight	37251.0 kDa
Excluded volume excluded_volume	46466 Å³
Envelope volume envelope_volume	53289 Å³
Hydration-shell volume shell_volume	21144 Å³
Envelope diameter envelope_diameter	77.7 Å
Shell Rg shell_rg	27.78 Å
Envelope Rg envelope_rg	21.92 Å
Shape Rg shape_rg	21.63 Å
Total Rg total_rg	22.59 Å
Total atoms total_atoms	2633
Residues n_residues	333
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	75.5 Å
Rg (real space) rg_real	22.63 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	2.4020e+07
I(0) uncertainty (real space) i0_real_error	3.3730e+05
Rg (reciprocal space) rg_reciprocal	22.62 Å
I(0) (reciprocal space) i0_reciprocal	24020000.0000
Solution quality estimate total_estimate	0.8613
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.2 Å
Skewness Skewness skewness	0.443
Kurtosis Kurtosis kurtosis	-0.341
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8293000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.751; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.981

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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-LIKE PROTEIN 2
Molecular weight formula_weight	17801.9 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,B
Atom count atom_count	3003

MATPASAPDTRALVADFVGYKLRQKGYVSGAGPGEGPAADPLGQALRAIGDEFETRFRRTFSDLAAQLHVTPGSAQQRFTQVSDELFQGGPNWGRLVAFFVFGAALCAESVNKEMEPLVGQVQEWMVEYLETRLADWIHSSGGWAEFTALYGDGALEEARRLR

来源 Source

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

Entity 2 Entity 2 polymer

Description description	BCL-2-LIKE PROTEIN 2
Molecular weight formula_weight	2336.6 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	P,Q

AADPLGQALRAIGDEFETRFR

来源 Source

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

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	277

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4cima_
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.1.4.1 — Bcl-2 inhibitors of programmed cell death

Domain ID domain_id	d4cimb_
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.1.4.1 — Bcl-2 inhibitors of programmed cell death

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8. Citations (1)

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Unit-cell length a length_a	41.922 Å
Unit-cell length b length_b	60.726 Å
Unit-cell length c length_c	67.098 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.85 °
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	1.500 Å
Low-resolution limit resolution_low	44.229 Å
R factor r_factor	0.1874
R_work r_work	0.1862
R_free r_free	0.2096

fit	/app/data/saxs_computation/ci/4cim/4cim.fit
pddf	/app/data/pr_computation/ci/4cim/4cim.pr.out
profile	/app/data/saxs_computation/ci/4cim/4cim.dat

Complex of a Bcl-w BH3 mutant with a BH3 domain

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

BCL-2-LIKE 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 (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) 2 domains

SCOP 2.08 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)