SAXSdb — 6mcy

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

Bcl-2 homologous antagonist/killer

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 21–184	Mutation：C154S	FMT FORMIC ACID × 3 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；281 K；20% PEG 3350, 200 mM ammonium formate	Resolution 1.75 Å R-free 0.218
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 21–184	Mutation：C154S	FMT FORMIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；281 K；20% PEG 3350, 200 mM ammonium formate	Resolution 1.75 Å R-free 0.218
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 21–184	Mutation：C154S	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；281 K；20% PEG 3350, 200 mM ammonium formate	Resolution 1.75 Å R-free 0.218
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 21–184	Mutation：C154S	FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；281 K；20% PEG 3350, 200 mM ammonium formate	Resolution 1.75 Å R-free 0.218

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 6MCY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2VOH Structure of mouse A1 bound to the Bak BH3-domain Deposited 2008-02-17	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 64–89（26 aa） Fragment：BH3-DOMAIN, RESIDUES 64-89	Not recorded	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
5KTG Crystal structure of mouse Bak BH3-in-groove homodimer (GFP) Deposited 2016-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 66–144（79 aa） Fragment：GFP, GS linker, BAK (UNP residues 66-144) Chain B 66–144（79 aa） Fragment：GFP, GS linker, BAK (UNP residues 66-144)	Non-standard monomer：Yes (specific site not provided by mmCIF) 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；293 K；7-12% PEG3350, 20% MPD, 100 mM Tris, pH 7.0-8.5, 0.5% CHAPS	Resolution 2.80 Å R-free 0.275
5KTG Crystal structure of mouse Bak BH3-in-groove homodimer (GFP) Deposited 2016-07-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 66–144（79 aa） Fragment：GFP, GS linker, BAK (UNP residues 66-144) Chain B 66–144（79 aa） Fragment：GFP, GS linker, BAK (UNP residues 66-144)	Non-standard monomer：Yes (specific site not provided by mmCIF) 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；293 K；7-12% PEG3350, 20% MPD, 100 mM Tris, pH 7.0-8.5, 0.5% CHAPS	Resolution 2.80 Å R-free 0.275

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

View Construct and Data Evidence

UniProt name	BAK_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–169； UniProt 21–184 Author chain B； PDBConstruct 6–169； UniProt 21–184 Author chain C； PDBConstruct 6–169； UniProt 21–184 Author chain D； PDBConstruct 6–169； UniProt 21–184

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	6mcy
Deposition date deposition_date	2018-09-03
Structure title title	Crystal structure of mouse Bak
Keywords keywords	Bcl-2 family, Bak, alpha-helical, 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	30.42 Å
Radius of gyration Rg (electron density) rg_electron	29.87 Å
Forward intensity I(0) i0	87536200.00
Molecular weight molecular_weight	74867.0 kDa
Excluded volume excluded_volume	93991 Å³
Envelope volume envelope_volume	115530 Å³
Hydration-shell volume shell_volume	33236 Å³
Envelope diameter envelope_diameter	117.8 Å
Shell Rg shell_rg	35.91 Å
Envelope Rg envelope_rg	29.94 Å
Shape Rg shape_rg	29.86 Å
Total Rg total_rg	30.46 Å
Total atoms total_atoms	5318
Residues n_residues	667
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	79.1 Å
Rg (real space) rg_real	28.87 Å
Rg uncertainty (real space) rg_real_error	0.13 Å
I(0) (real space) i0_real	8.3800e+07
I(0) uncertainty (real space) i0_real_error	8.2550e+05
Rg (reciprocal space) rg_reciprocal	30.46 Å
I(0) (reciprocal space) i0_reciprocal	87530000.0000
Solution quality estimate total_estimate	0.6882
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.0 Å
Skewness Skewness skewness	0.199
Kurtosis Kurtosis kurtosis	-0.640
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.9075
Highest regularization parameter α highest_alpha	32330000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.996; Stabil: 0.987; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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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 homologous antagonist/killer
Molecular weight formula_weight	18968.2 kDa
Mutation mutation	C154S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5963

GPLGSSEQQVAQDTEEVFRSYVFYLHQQEQETQGAAAPANPEMDNLPLEPNSILGQVGRQLALIGDDINRRYDTEFQNLLEQLQPTAGNAYELFTKIASSLFKSGISWGRVVALLGFGYRLALYVYQRGLTGFLGQVTSFLADIILHHYIARWIAQRGGWVAALNFRRD

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 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	7

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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	420

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6mcya1
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	d6mcya2
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	d6mcyb1
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	d6mcyb2
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	d6mcyc1
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	d6mcyc2
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	d6mcyd1
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	d6mcyd2
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 (4 domains)

Domain ID domain_id	6mcyA01
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	6mcyB01
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	6mcyC01
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	6mcyD01
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	36.951 Å
Unit-cell length b length_b	59.261 Å
Unit-cell length c length_c	79.207 Å
Unit-cell angle α angle_alpha	93.14 °
Unit-cell angle β angle_beta	93.35 °
Unit-cell angle γ angle_gamma	97.63 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.748 Å
Low-resolution limit resolution_low	36.543 Å
R factor r_factor	0.1820
R_work r_work	0.1809
R_free r_free	0.2178

fit	/app/data/saxs_computation/mc/6mcy/6mcy.fit
pddf	/app/data/pr_computation/mc/6mcy/6mcy.pr.out
profile	/app/data/saxs_computation/mc/6mcy/6mcy.dat

Crystal structure of mouse Bak

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

Bcl-2 homologous antagonist/killer

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