SAXSdb — 7nk0

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

Baculoviral IAP repeat-containing protein 3

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 26–102	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；12 % w/v Polyethylene glycol 8,000, 10 % w/v Glycerol, 500 mM Potassium chloride	Resolution 3.30 Å R-free 0.356
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 26–102	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；12 % w/v Polyethylene glycol 8,000, 10 % w/v Glycerol, 500 mM Potassium chloride	Resolution 3.30 Å R-free 0.356

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 7NK0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2UVL Human BIR3 domain of Baculoviral Inhibitor of Apoptosis Repeat- Containing 3 (BIRC3) Deposited 2007-03-12	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 244–337（94 aa） Fragment：BIR3 DOMAIN, RESIDUES 244-337 Chain B 244–337（94 aa） Fragment：BIR3 DOMAIN, RESIDUES 244-337	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 16% PEG 8000 40MM KPO4 20% GLYCEROL	Resolution 1.91 Å R-free 0.240
3EB5 Structure of the cIAP2 RING domain Deposited 2008-08-27	Different construct 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 536–604（69 aa） Fragment：RING domain (UNP residues 536 to 604)	Not recorded	ZN ZINC ION × 4 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；291 K；0.4 M NH4(SO4)2, 1 M LiSO4, 0.1 M Na Citrate, pH 6.2, vapor diffusion, hanging drop, temperature 291K	Resolution 2.00 Å R-free 0.275
3EB6 Structure of the cIAP2 RING domain bound to UbcH5b Deposited 2008-08-27	Different construct 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 536–604（69 aa） Fragment：RING domain (RESIDUES 536 TO 604)	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；291 K；3.3 M NaCl, 0.1 M HEPES, pH 7.3, vapor diffusion, hanging drop, temperature 291K	Resolution 3.40 Å R-free 0.320
3M0A Crystal structure of TRAF2:cIAP2 complex Deposited 2010-03-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 26–99（74 aa） Fragment：Residues 26-99	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；8% PEG 3350, 6% Tacsimate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.61 Å R-free 0.268
3M0D Crystal structure of the TRAF1:TRAF2:cIAP2 complex Deposited 2010-03-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 26–99（74 aa） Fragment：Residues 26-99	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.15M AmSO4, 0.1M MES, 15% PEG 4000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.247
3M0D Crystal structure of the TRAF1:TRAF2:cIAP2 complex Deposited 2010-03-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 26–99（74 aa） Fragment：Residues 26-99	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.15M AmSO4, 0.1M MES, 15% PEG 4000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.247

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BIRC3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain D； PDBConstruct 22–98； UniProt 26–102 Author chain E； PDBConstruct 22–98； UniProt 26–102

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	7nk0
Deposition date deposition_date	2021-02-17
Structure title title	Structure of the BIR1 domain of cIAP2
Keywords keywords	Baculoviral IAP Repeat, Inhibitor of Apoptosis Protein, E3 ligase, 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	18.58 Å
Radius of gyration Rg (electron density) rg_electron	18.14 Å
Forward intensity I(0) i0	5180070.00
Molecular weight molecular_weight	16198.0 kDa
Excluded volume excluded_volume	19981 Å³
Envelope volume envelope_volume	23783 Å³
Hydration-shell volume shell_volume	11863 Å³
Envelope diameter envelope_diameter	60.9 Å
Shell Rg shell_rg	22.51 Å
Envelope Rg envelope_rg	18.28 Å
Shape Rg shape_rg	18.19 Å
Total Rg total_rg	18.70 Å
Total atoms total_atoms	1125
Residues n_residues	148
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	60.8 Å
Rg (real space) rg_real	18.69 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	5.1800e+06
I(0) uncertainty (real space) i0_real_error	6.4270e+04
Rg (reciprocal space) rg_reciprocal	18.67 Å
I(0) (reciprocal space) i0_reciprocal	5180000.0000
Solution quality estimate total_estimate	0.7853
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.7 Å
Skewness Skewness skewness	0.409
Kurtosis Kurtosis kurtosis	-0.531
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	909700.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.791; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.835; Smooth: 0.000

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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	Baculoviral IAP repeat-containing protein 3
Molecular weight formula_weight	11053.6 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E
Atom count atom_count	1130

MGSSHHHHHHSSGLVPRGSHMLSCELYRMSTYSTFPAGVPVSERSLARAGFYYTGVNDKVKCFCCGLMLDNWKRGDSPTEKHKKLYPSCRFVQSLNSV

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 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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8. Citations (1)

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Unit-cell length a length_a	93.430 Å
Unit-cell length b length_b	93.430 Å
Unit-cell length c length_c	42.430 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	12

Space group space_group	P 64
Space-group number int_tables_number	172
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	46.720 Å
R factor r_factor	0.2978
R_work r_work	0.2948
R_free r_free	0.3558

fit	/app/data/saxs_computation/nk/7nk0/7nk0.fit
pddf	/app/data/pr_computation/nk/7nk0/7nk0.pr.out
profile	/app/data/saxs_computation/nk/7nk0/7nk0.dat

Structure of the BIR1 domain of cIAP2

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

Baculoviral IAP repeat-containing protein 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