SAXSdb — 3eb6

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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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 536–604	Fragment：RING domain (RESIDUES 536 TO 604)	Ubiquitin-conjugating enzyme E2 D2 × 2 （P62840） 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

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 3EB6	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
3M0A Crystal structure of TRAF2:cIAP2 complex Deposited 2010-03-02	Different construct Different ligand/ion 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 ligand/ion 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 ligand/ion 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
7NK0 Structure of the BIR1 domain of cIAP2 Deposited 2021-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 26–102（77 aa）	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
7NK0 Structure of the BIR1 domain of cIAP2 Deposited 2021-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 26–102（77 aa）	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

5 other PDB entries and 7 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 A； PDBConstruct 6–74； UniProt 536–604

Ubiquitin-conjugating enzyme E2 D2

Xenopus laevis

UniProt P62840

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 1–147	Not recorded	Baculoviral IAP repeat-containing protein 3 × 2 （Q13489） 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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	UB2D2_XENLA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–149； UniProt 1–147

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	3eb6
Deposition date deposition_date	2008-08-27
Structure title title	Structure of the cIAP2 RING domain bound to UbcH5b
Keywords keywords	RING domain, E2, Apoptosis, Metal-binding, Zinc-finger, Ligase, Ubl conjugation pathway; APOPTOSIS, LIGASE
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	20.69 Å
Radius of gyration Rg (electron density) rg_electron	19.88 Å
Forward intensity I(0) i0	10835100.00
Molecular weight molecular_weight	24294.0 kDa
Excluded volume excluded_volume	30356 Å³
Envelope volume envelope_volume	37288 Å³
Hydration-shell volume shell_volume	16508 Å³
Envelope diameter envelope_diameter	73.5 Å
Shell Rg shell_rg	25.21 Å
Envelope Rg envelope_rg	20.16 Å
Shape Rg shape_rg	19.87 Å
Total Rg total_rg	20.72 Å
Total atoms total_atoms	1693
Residues n_residues	213
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	70.9 Å
Rg (real space) rg_real	20.72 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	1.0840e+07
I(0) uncertainty (real space) i0_real_error	1.5920e+05
Rg (reciprocal space) rg_reciprocal	20.71 Å
I(0) (reciprocal space) i0_reciprocal	10840000.0000
Solution quality estimate total_estimate	0.7970
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	20.6 Å
Skewness Skewness skewness	0.352
Kurtosis Kurtosis kurtosis	-0.365
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1989000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.925; 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	8238.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1693

LGSGTTEDVSDLPVEEQLRRLQEERTCKVCMDKEVSIVFIPCGHLVVCKDCAPSLRKCPICRSTIKGTVRTFLS

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	Ubiquitin-conjugating enzyme E2 D2
Molecular weight formula_weight	16899.4 kDa
EC 编号 ec_number	6.3.2.19
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSMALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM

来源 Source

来源生物 organism	Xenopus laevis
通用名 common_name	clawed frog, platanna
NCBI Class编号 ncbi_taxonomy_id	8355
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

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

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3eb6b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.1 — UBC-related

Domain ID domain_id	d3eb6b2
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	3eb6A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3eb6B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

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8. Citations (1)

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Unit-cell length a length_a	137.226 Å
Unit-cell length b length_b	137.226 Å
Unit-cell length c length_c	111.870 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 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	58.520 Å
R factor r_factor	0.2830
R_work r_work	0.2810
R_free r_free	0.3200

fit	/app/data/saxs_computation/eb/3eb6/3eb6.fit
pddf	/app/data/pr_computation/eb/3eb6/3eb6.pr.out
profile	/app/data/saxs_computation/eb/3eb6/3eb6.dat

Structure of the cIAP2 RING domain bound to UbcH5b

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

Ubiquitin-conjugating enzyme E2 D2

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

来源 Source

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)