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3eb5

Structure of the cIAP2 RING domain

Method: X-RAY DIFFRACTION Dmax: 50.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Baculoviral IAP repeat-containing protein 3

Homo sapiens

UniProt Q13489

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 A； UniProt 536–604 Fragment：RING domain (UNP residues 536 to 604) 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

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 3EB5 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 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
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 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 oligomeric state 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 oligomeric state 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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3eb5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3eb5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3eb5
Deposition date deposition_date2008-08-27
Structure title titleStructure of the cIAP2 RING domain
Keywords keywordsRING domain, Apoptosis, Metal-binding, Zinc-finger; APOPTOSIS
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.90 Å
Radius of gyration Rg (electron density) rg_electron13.19 Å
Forward intensity I(0) i01353350.00
Molecular weight molecular_weight7524.0 kDa
Excluded volume excluded_volume9316 ų
Envelope volume envelope_volume11043 ų
Hydration-shell volume shell_volume7864 ų
Envelope diameter envelope_diameter49.3 Å
Shell Rg shell_rg17.36 Å
Envelope Rg envelope_rg13.75 Å
Shape Rg shape_rg13.26 Å
Total Rg total_rg14.03 Å
Total atoms total_atoms512
Residues n_residues65
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax50.1 Å
Rg (real space) rg_real13.97 Å
Rg uncertainty (real space) rg_real_error0.53 Å
I(0) (real space) i0_real1.3530e+06
I(0) uncertainty (real space) i0_real_error1.7080e+04
Rg (reciprocal space) rg_reciprocal13.96 Å
I(0) (reciprocal space) i0_reciprocal1353000.0000
Solution quality estimate total_estimate0.8461
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.2 Å
Skewness Skewness skewness0.446
Kurtosis Kurtosis kurtosis-0.119
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha115000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.736; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.805; Smooth: 0.983
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id3eb5A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
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8. Citations (1)

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9. Files and Curves (10)