SAXSdb — 1f3v

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

TUMOR NECROSIS FACTOR RECEPTOR TYPE 1 ASSOCIATED DEATH DOMAIN PROTEIN

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–179	Fragment：N-TERMINAL DOMAIN	TUMOR NECROSIS FACTOR RECEPTOR-ASSOCIATED PROTEIN × 1 （Q12933）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.261

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 1F3V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1F2H SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF THE TNFR1 ASSOCIATED PROTEIN, TRADD. Deposited 2000-05-24	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–169（169 aa） Fragment：N-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.6；298 K；Ionic strength (raw mmCIF value) 200mM NaCl；Pressure 1 NMR measurement conditions pH 6.6；298 K；Ionic strength (raw mmCIF value) 200mM NaCl；Pressure 1 NMR measurement conditions pH 6.6；298 K；Ionic strength (raw mmCIF value) 200mM NaCl；Pressure 1 NMR sample composition 1.0 mM 15N N-TRADD \| 20mM Imidazole pH 6.6 200 mMNaCL 20 mM DTT 0.05%NaN3 90%H2O 10% D2O NMR sample composition 1.1 mM 15N/13C N-TRADD \| 20mM Imidazole pH 6.6 200 mMNaCL 20 mM DTT 0.05%NaN3 90%H2O 10% D2O NMR sample composition 0.8 mM 15N/13C N-TRADD \| 20mM Imidazole pH 6.6 200 mMNaCL 220 mM DTT 0.05%NaN3 100% D2O	Resolution not provided
5XME Solution structure of C-terminal domain of TRADD Deposited 2017-05-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 199–312（114 aa） Fragment：UNP RESIDUES 199-312	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；301 K；Pressure 1 NMR sample composition 0.6 mM U-99% 13C; U-99% 15N;U-98% 2H TRADD DD, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6AC0 Crystal structure of TRADD death domain GlcNAcylated by EPEC effector NleB Deposited 2018-07-24	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 A 195–312（118 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；1.6 M Na/KPO4, pH 6.0	Resolution 1.45 Å R-free 0.224
7CSQ Solution structure of the complex between p75NTR-DD and TRADD-DD Deposited 2020-08-16	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 199–312（114 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；301 K；Pressure 1 NMR sample composition 0.2 mM [U-99% 13C; U-99% 15N] p75 neurotrophin receptor death domain, 2 mM [U-99% 13C; U-99% 15N] tumor necrosis factor receptor1-associated death domain protein, 50% H2O/50% D2O \| 50% H2O/50% D2O	Resolution not provided
9VGD Helical assembly of TRADD death domain Deposited 2025-06-13	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 28 PDB declaration: 28-meric	Chain A 199–312（114 aa） Chain B 199–312（114 aa） Chain C 199–312（114 aa） Chain E 199–312（114 aa） Chain F 199–312（114 aa） Chain H 199–312（114 aa） Chain I 199–312（114 aa） Chain J 199–312（114 aa） Chain K 199–312（114 aa） Chain M 199–312（114 aa） Chain N 199–312（114 aa） Chain Q 199–312（114 aa） Chain R 199–312（114 aa） Chain S 199–312（114 aa） Chain T 199–312（114 aa） Chain V 199–312（114 aa） Chain W 199–312（114 aa） Chain Y 199–312（114 aa） Chain Z 199–312（114 aa） Chain b 199–312（114 aa） Chain c 199–312（114 aa） Chain e 199–312（114 aa） Chain f 199–312（114 aa） Chain g 199–312（114 aa） Chain h 199–312（114 aa） Chain j 199–312（114 aa） Chain k 199–312（114 aa） Chain l 199–312（114 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9VIN Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD Deposited 2025-06-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 31 PDB declaration: 31-meric	Chain E 199–312（114 aa） Chain F 199–312（114 aa） Chain N 199–312（114 aa） Chain V 199–312（114 aa） Chain W 199–312（114 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；100 mM NaCl, 20 mM Tris-HCl pH7.5, 1mM EDTA, 1mM DTT. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.41 Å

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

View Construct and Data Evidence

UniProt name	TRADD_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–179； UniProt 1–179

TUMOR NECROSIS FACTOR RECEPTOR-ASSOCIATED PROTEIN

Homo sapiens

UniProt Q12933

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 331–501	Fragment：TRAF DOMAIN Non-standard monomer：Yes (specific site not provided by mmCIF)	TUMOR NECROSIS FACTOR RECEPTOR TYPE 1 ASSOCIATED DEATH DOMAIN PROTEIN × 1 （Q15628）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.261

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 1F3V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CA4 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) Deposited 1999-02-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 334–501（168 aa） Fragment：TRAF DOMAIN Chain B 334–501（168 aa） Fragment：TRAF DOMAIN Chain C 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.20 Å R-free 0.251
1CA4 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) Deposited 1999-02-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 334–501（168 aa） Fragment：TRAF DOMAIN Chain E 334–501（168 aa） Fragment：TRAF DOMAIN Chain F 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.20 Å R-free 0.251
1CA9 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A PEPTIDE FROM TNF-R2 Deposited 1999-02-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 310–501（192 aa） Fragment：TRAF DOMAIN Chain B 310–501（192 aa） Fragment：TRAF DOMAIN Chain C 310–501（192 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.30 Å R-free 0.289
1CA9 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A PEPTIDE FROM TNF-R2 Deposited 1999-02-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 310–501（192 aa） Fragment：TRAF DOMAIN Chain E 310–501（192 aa） Fragment：TRAF DOMAIN Chain F 310–501（192 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.30 Å R-free 0.289
1CA9 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A PEPTIDE FROM TNF-R2 Deposited 1999-02-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 310–501（192 aa） Fragment：TRAF DOMAIN Chain B 310–501（192 aa） Fragment：TRAF DOMAIN Chain C 310–501（192 aa） Fragment：TRAF DOMAIN Chain D 310–501（192 aa） Fragment：TRAF DOMAIN Chain E 310–501（192 aa） Fragment：TRAF DOMAIN Chain F 310–501（192 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.30 Å R-free 0.289
1CZY CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE TRAF DOMAIN OF HUMAN TRAF2 AND AN LMP1 BINDING PEPTIDE Deposited 1999-09-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 334–501（168 aa） Fragment：TRAF DOMAIN Chain B 334–501（168 aa） Fragment：TRAF DOMAIN Chain C 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES BUFFER, pH 6.00, VAPOR DIFFUSION, temperature 20K	Resolution 2.00 Å R-free 0.245
1CZZ STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A 17-RESIDUE CD40 PEPTIDE Deposited 1999-09-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 315–501（187 aa） Fragment：TRAF DOMAIN Chain B 315–501（187 aa） Fragment：TRAF DOMAIN Chain C 315–501（187 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；293 K；PEG4K, MES, PH 5.6, VAPOR DIFFUSION, temperature 293K	Resolution 2.70 Å R-free 0.267
1D01 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A HUMAN CD30 PEPTIDE Deposited 1999-09-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 334–501（168 aa） Fragment：TRAF DOMAIN Chain B 334–501（168 aa） Fragment：TRAF DOMAIN Chain C 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 20K	Resolution 2.00 Å R-free 0.244
1D01 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A HUMAN CD30 PEPTIDE Deposited 1999-09-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 334–501（168 aa） Fragment：TRAF DOMAIN Chain E 334–501（168 aa） Fragment：TRAF DOMAIN Chain F 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 20K	Resolution 2.00 Å R-free 0.244
1D0A STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE Deposited 1999-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 334–501（168 aa） Fragment：TRAF DOMAIN Chain B 334–501（168 aa） Fragment：TRAF DOMAIN Chain C 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.251
1D0A STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE Deposited 1999-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 334–501（168 aa） Fragment：TRAF DOMAIN Chain E 334–501（168 aa） Fragment：TRAF DOMAIN Chain F 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.251
1D0A STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE Deposited 1999-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 334–501（168 aa） Fragment：TRAF DOMAIN Chain B 334–501（168 aa） Fragment：TRAF DOMAIN Chain C 334–501（168 aa） Fragment：TRAF DOMAIN Chain D 334–501（168 aa） Fragment：TRAF DOMAIN Chain E 334–501（168 aa） Fragment：TRAF DOMAIN Chain F 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.251
1D0A STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE Deposited 1999-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 334–501（168 aa） Fragment：TRAF DOMAIN Chain B 334–501（168 aa） Fragment：TRAF DOMAIN Chain C 334–501（168 aa） Fragment：TRAF DOMAIN Chain D 334–501（168 aa） Fragment：TRAF DOMAIN Chain E 334–501（168 aa） Fragment：TRAF DOMAIN Chain F 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES, PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.251
1D0J STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M4-1BB PEPTIDE Deposited 1999-09-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 334–501（168 aa） Fragment：TRAF DOMAIN Chain B 334–501（168 aa） Fragment：TRAF DOMAIN Chain C 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.50 Å R-free 0.270
1D0J STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M4-1BB PEPTIDE Deposited 1999-09-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 334–501（168 aa） Fragment：TRAF DOMAIN Chain E 334–501（168 aa） Fragment：TRAF DOMAIN Chain F 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.50 Å R-free 0.270
1D0J STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M4-1BB PEPTIDE Deposited 1999-09-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 334–501（168 aa） Fragment：TRAF DOMAIN Chain B 334–501（168 aa） Fragment：TRAF DOMAIN Chain C 334–501（168 aa） Fragment：TRAF DOMAIN Chain D 334–501（168 aa） Fragment：TRAF DOMAIN Chain E 334–501（168 aa） Fragment：TRAF DOMAIN Chain F 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.50 Å R-free 0.270
1D0J STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M4-1BB PEPTIDE Deposited 1999-09-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 334–501（168 aa） Fragment：TRAF DOMAIN Chain B 334–501（168 aa） Fragment：TRAF DOMAIN Chain C 334–501（168 aa） Fragment：TRAF DOMAIN Chain D 334–501（168 aa） Fragment：TRAF DOMAIN Chain E 334–501（168 aa） Fragment：TRAF DOMAIN Chain F 334–501（168 aa） Fragment：TRAF DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；PEG4K, MES PH 6.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.50 Å R-free 0.270
1QSC CRYSTAL STRUCTURE OF THE TRAF DOMAIN OF TRAF2 IN A COMPLEX WITH A PEPTIDE FROM THE CD40 RECEPTOR Deposited 1999-06-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 311–501（191 aa） Fragment：TRAF DOMAIN Chain B 311–501（191 aa） Fragment：TRAF DOMAIN Chain C 311–501（191 aa） Fragment：TRAF DOMAIN	Non-standard monomer：Yes (specific site not provided by mmCIF) 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；pH 7；298 K；MME-PEG 2000, MAGNESIUM CHLORIDE, BISTRIS PROPANE, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298.00K	Resolution 2.40 Å R-free 0.257
3KNV Crystal structure of the RING and first zinc finger domains of TRAF2 Deposited 2009-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–133（133 aa） Fragment：RING and the first zinc finger domains: UNP residues 1-133	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG 8000, 0.1 M HEPES pH 7.5, 8% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.239
3M06 Crystal Structure of TRAF2 Deposited 2010-03-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 266–329（64 aa） Fragment：Residues 266-329 Chain B 266–329（64 aa） Fragment：Residues 266-329 Chain C 266–329（64 aa） Fragment：Residues 266-329	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；8% PEG3350, 6% Tacsimate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.67 Å R-free 0.233
3M06 Crystal Structure of TRAF2 Deposited 2010-03-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 266–329（64 aa） Fragment：Residues 266-329 Chain E 266–329（64 aa） Fragment：Residues 266-329 Chain F 266–329（64 aa） Fragment：Residues 266-329	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；8% PEG3350, 6% Tacsimate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.67 Å R-free 0.233
3M0A Crystal structure of TRAF2:cIAP2 complex Deposited 2010-03-02	Different construct Different mutation/modification 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 266–329（64 aa） Fragment：Residues 266-329 Chain B 266–329（64 aa） Fragment：Residues 266-329 Chain C 266–329（64 aa） Fragment：Residues 266-329	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 mutation/modification 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 266–329（64 aa） Fragment：Residues 266-329 Chain B 266–329（64 aa） Fragment：Residues 266-329	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 266–329（64 aa） Fragment：Residues 266-329 Chain B 266–329（64 aa） Fragment：Residues 266-329	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
8T5Q SARS-CoV-2 ORF3a peptide in complex with TRAF2 TRAF domain Deposited 2023-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 315–501（187 aa） Fragment：TRAF domain (UNP residues 315-501) Chain B 315–501（187 aa） Fragment：TRAF domain (UNP residues 315-501) Chain C 315–501（187 aa） Fragment：TRAF domain (UNP residues 315-501)	Not recorded	PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277.15 K；0.1 M sodium citrate, pH 5.0, 20% w/v PEG8000	Resolution 1.90 Å R-free 0.240
8T5Q SARS-CoV-2 ORF3a peptide in complex with TRAF2 TRAF domain Deposited 2023-06-14	Different construct Different mutation/modification 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 315–501（187 aa） Fragment：TRAF domain (UNP residues 315-501) Chain E 315–501（187 aa） Fragment：TRAF domain (UNP residues 315-501) Chain F 315–501（187 aa） Fragment：TRAF domain (UNP residues 315-501)	Not recorded	PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277.15 K；0.1 M sodium citrate, pH 5.0, 20% w/v PEG8000	Resolution 1.90 Å R-free 0.240

13 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRAF2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–171； UniProt 331–501

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	1f3v
Deposition date deposition_date	2000-06-06
Structure title title	Crystal structure of the complex between the N-terminal domain of TRADD and the TRAF domain of TRAF2
Keywords keywords	a-b sandwich, 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	22.16 Å
Radius of gyration Rg (electron density) rg_electron	21.08 Å
Forward intensity I(0) i0	23801300.00
Molecular weight molecular_weight	36474.0 kDa
Excluded volume excluded_volume	45310 Å³
Envelope volume envelope_volume	54914 Å³
Hydration-shell volume shell_volume	21944 Å³
Envelope diameter envelope_diameter	81.0 Å
Shell Rg shell_rg	27.41 Å
Envelope Rg envelope_rg	21.44 Å
Shape Rg shape_rg	21.04 Å
Total Rg total_rg	22.05 Å
Total atoms total_atoms	2541
Residues n_residues	322
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	75.3 Å
Rg (real space) rg_real	22.11 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	2.3800e+07
I(0) uncertainty (real space) i0_real_error	3.4780e+05
Rg (reciprocal space) rg_reciprocal	22.12 Å
I(0) (reciprocal space) i0_reciprocal	23800000.0000
Solution quality estimate total_estimate	0.7917
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	66.3 Å
Skewness Skewness skewness	0.329
Kurtosis Kurtosis kurtosis	-0.135
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3592000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.769; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; 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	TUMOR NECROSIS FACTOR RECEPTOR TYPE 1 ASSOCIATED DEATH DOMAIN PROTEIN
Molecular weight formula_weight	19413.0 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	2749

MAAGQNGHEEWVGSAYLFVESSLDKVVLSDAYAHPQQKVAVYRALQAALAESGGSPDVLQMLKIHRSDPQLIVQLRFCGRQPCGRFLRAYREGALRAALQRSLAAALAQHSVPLQLELRAGAERLDALLADEERCLSCILAQQPDRLRDEELAELEDALRNLKCGSGARGGDGEVASAP

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	TUMOR NECROSIS FACTOR RECEPTOR-ASSOCIATED PROTEIN
Molecular weight formula_weight	19718.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

KDLAMADLEQKVLEMEASTYDGVFIWKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKMEAKNSYVRDDAIFIKAIVDLTGL

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	208

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1f3va_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.22 — TRADD, N-terminal domain
Family Family family	d.58.22.1 — TRADD, N-terminal domain

Domain ID domain_id	d1f3vb1
Class class	b — All beta proteins
Fold Fold fold	b.8 — TRAF domain-like
Superfamily Superfamily superfamily	b.8.1 — TRAF domain-like
Family Family family	b.8.1.1 — MATH domain

Domain ID domain_id	d1f3vb2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.2 — Trimerization domain of TRAF
Family Family family	h.1.2.1 — Trimerization domain of TRAF

CATH v4.4 (2 domains)

Domain ID domain_id	1f3vA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	680 — TRADD, N-terminal domain

Domain ID domain_id	1f3vB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily	10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A

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8. Citations (1)

▶

Unit-cell length a length_a	132.400 Å
Unit-cell length b length_b	132.400 Å
Unit-cell length c length_c	62.800 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	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2290
R_free r_free	0.2610

fit	/app/data/saxs_computation/f3/1f3v/1f3v.fit
pddf	/app/data/pr_computation/f3/1f3v/1f3v.pr.out
profile	/app/data/saxs_computation/f3/1f3v/1f3v.dat

Crystal structure of the complex between the N-terminal domain of TRADD and the TRAF domain of TRAF2

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

TUMOR NECROSIS FACTOR RECEPTOR TYPE 1 ASSOCIATED DEATH DOMAIN PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

TUMOR NECROSIS FACTOR RECEPTOR-ASSOCIATED PROTEIN

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 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)