1d0a

STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE

Method: X-RAY DIFFRACTION D_max: 129.6 Å Quality: GOOD

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

TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 334–501 Chain B； UniProt 334–501 Chain C； UniProt 334–501	Fragment：TRAF DOMAIN	OX40L RECEPTOR PEPTIDE × 3 （P43489）	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
2	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain D； UniProt 334–501 Chain E； UniProt 334–501 Chain F； UniProt 334–501	Fragment：TRAF DOMAIN	OX40L RECEPTOR PEPTIDE × 3 （P43489）	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
3	Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 334–501 Chain B； UniProt 334–501 Chain C； UniProt 334–501 Chain D； UniProt 334–501 Chain E； UniProt 334–501 Chain F； UniProt 334–501	Fragment：TRAF DOMAIN	OX40L RECEPTOR PEPTIDE × 6 （P43489）	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
4	Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 334–501 Chain B； UniProt 334–501 Chain C； UniProt 334–501 Chain D； UniProt 334–501 Chain E； UniProt 334–501 Chain F； UniProt 334–501	Fragment：TRAF DOMAIN	OX40L RECEPTOR PEPTIDE × 6 （P43489）	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

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 1D0A	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 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 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 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 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 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 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 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 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 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
1D0J STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M4-1BB PEPTIDE Deposited 1999-09-10	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 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 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 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
1F3V Crystal structure of the complex between the N-terminal domain of TRADD and the TRAF domain of TRAF2 Deposited 2000-06-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 331–501（171 aa） Fragment：TRAF DOMAIN	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；293 K；VAPOR DIFFUSION, temperature 293K	Resolution 2.00 Å R-free 0.261
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 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 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 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 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 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 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 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRAF2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–168； UniProt 334–501 Author chain B； PDBConstruct 1–168； UniProt 334–501 Author chain C； PDBConstruct 1–168； UniProt 334–501 Author chain D； PDBConstruct 1–168； UniProt 334–501 Author chain E； PDBConstruct 1–168； UniProt 334–501 Author chain F； PDBConstruct 1–168； UniProt 334–501

OX40L RECEPTOR PEPTIDE

OrganismNot specified

UniProt P43489

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain G； UniProt 262–266 Chain H； UniProt 262–266 Chain I； UniProt 262–266	Fragment：TRAF-BINDING SEQUENCE Non-standard monomer：Yes (specific site not provided by mmCIF)	TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2 × 3 （Q12933）	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
2	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain J； UniProt 262–266 Chain K； UniProt 262–266 Chain L； UniProt 262–266	Fragment：TRAF-BINDING SEQUENCE Non-standard monomer：Yes (specific site not provided by mmCIF)	TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2 × 3 （Q12933）	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
3	Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain G； UniProt 262–266 Chain H； UniProt 262–266 Chain I； UniProt 262–266 Chain J； UniProt 262–266 Chain K； UniProt 262–266 Chain L； UniProt 262–266	Fragment：TRAF-BINDING SEQUENCE Non-standard monomer：Yes (specific site not provided by mmCIF)	TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2 × 6 （Q12933）	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
4	Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain G； UniProt 262–266 Chain H； UniProt 262–266 Chain I； UniProt 262–266 Chain J； UniProt 262–266 Chain K； UniProt 262–266 Chain L； UniProt 262–266	Fragment：TRAF-BINDING SEQUENCE Non-standard monomer：Yes (specific site not provided by mmCIF)	TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2 × 6 （Q12933）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1D0A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2HEV Crystal structure of the complex between OX40L and OX40 Deposited 2006-06-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 29–170（142 aa） Fragment：extracellular domain (residues 29-170)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；8% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.41 Å R-free 0.251
2HEY Crystal structure of murine OX40L bound to human OX40 Deposited 2006-06-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 29–170（142 aa） Fragment：extracellular domain (residues 29-170)	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；0.1 M NaCl, 1.4 M Ammonium Sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.00 Å R-free 0.247
2HEY Crystal structure of murine OX40L bound to human OX40 Deposited 2006-06-22	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain T 29–170（142 aa） Fragment：extracellular domain (residues 29-170)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；0.1 M NaCl, 1.4 M Ammonium Sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.00 Å R-free 0.247
6OGX Ternary complex of OX40R (TNFRSF4) bound to Fab1 and Fab2 Deposited 2019-04-03	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 G 29–170（142 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M Tris pH 8.5, 1.5 M D-L malic acid pH 7.0, 0.15 mM dimethylethylammonium propane sulfate (NDSB-195)	Resolution 2.77 Å R-free 0.254
6OKM Human OX40R (TNFRSF4) bound to Fab 3C8 Deposited 2019-04-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain R 29–170（142 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K	Resolution 2.10 Å R-free 0.238
6OKN OX40R (TNFRSF4) bound to Fab 1A7 Deposited 2019-04-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain R 29–170（142 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；tbd	Resolution 3.25 Å R-free 0.228
6OKN OX40R (TNFRSF4) bound to Fab 1A7 Deposited 2019-04-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 29–170（142 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；tbd	Resolution 3.25 Å R-free 0.228
7YK4 ox40-antibody Deposited 2022-07-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 29–170（142 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M potassium sodium tartrate, 14% PEG 3350, 10% glycerol	Resolution 2.70 Å R-free 0.298
7YK4 ox40-antibody Deposited 2022-07-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 29–170（142 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M potassium sodium tartrate, 14% PEG 3350, 10% glycerol	Resolution 2.70 Å R-free 0.298
8AG1 Crystal structure of a novel OX40 antibody Deposited 2022-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 29–170（142 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5；293 K；0.1m CITRATE, PH5.6, 2% TACSIMATE, 16% PEG3350	Resolution 3.30 Å R-free 0.268
8AG1 Crystal structure of a novel OX40 antibody Deposited 2022-07-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain a 29–170（142 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5；293 K；0.1m CITRATE, PH5.6, 2% TACSIMATE, 16% PEG3350	Resolution 3.30 Å R-free 0.268

7 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TNR4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 2–6； UniProt 262–266 Author chain H； PDBConstruct 2–6； UniProt 262–266 Author chain I； PDBConstruct 2–6； UniProt 262–266 Author chain J； PDBConstruct 2–6； UniProt 262–266 Author chain K； PDBConstruct 2–6； UniProt 262–266 Author chain L； PDBConstruct 2–6； UniProt 262–266

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1d0a
Deposition date deposition_date	1999-09-09
Structure title title	STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE
Keywords keywords	B-SANDWICH, PROTEIN-PEPTIDE COMPLEX, 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	41.47 Å
Radius of gyration Rg (electron density) rg_electron	40.74 Å
Forward intensity I(0) i0	185168000.00
Molecular weight molecular_weight	113190.0 kDa
Excluded volume excluded_volume	142460 Å³
Envelope volume envelope_volume	208090 Å³
Hydration-shell volume shell_volume	42382 Å³
Envelope diameter envelope_diameter	128.7 Å
Shell Rg shell_rg	47.59 Å
Envelope Rg envelope_rg	38.35 Å
Shape Rg shape_rg	40.73 Å
Total Rg total_rg	41.15 Å
Total atoms total_atoms	7968
Residues n_residues	1038
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	129.6 Å
Rg (real space) rg_real	41.38 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	1.8520e+08
I(0) uncertainty (real space) i0_real_error	3.0880e+06
Rg (reciprocal space) rg_reciprocal	41.47 Å
I(0) (reciprocal space) i0_reciprocal	185200000.0000
Solution quality estimate total_estimate	0.8911
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	61.4 Å
Skewness Skewness skewness	0.046
Kurtosis Kurtosis kurtosis	-0.805
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18130000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.845

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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 ASSOCIATED PROTEIN 2
Molecular weight formula_weight	19033.0 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	8683

AMADLEQKVLEMEASTYDGVFIWKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKMEAKNSYVRDDAIFIKAIVDLTGL

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	OX40L RECEPTOR PEPTIDE
Molecular weight formula_weight	640.7 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L

XPIQEE

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	715

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7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1d0aa1
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	d1d0aa2
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

Domain ID domain_id	d1d0ab1
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	d1d0ab2
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

Domain ID domain_id	d1d0ac1
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	d1d0ac2
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

Domain ID domain_id	d1d0ad1
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	d1d0ad2
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

Domain ID domain_id	d1d0ae1
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	d1d0ae2
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

Domain ID domain_id	d1d0af1
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	d1d0af2
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 (6 domains)

Domain ID domain_id	1d0aA00
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

Domain ID domain_id	1d0aB00
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

Domain ID domain_id	1d0aC00
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

Domain ID domain_id	1d0aD00
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

Domain ID domain_id	1d0aE00
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

Domain ID domain_id	1d0aF00
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 (2)

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Unit-cell length a length_a	136.400 Å
Unit-cell length b length_b	85.600 Å
Unit-cell length c length_c	125.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2250
R_work r_work	0.2250
R_free r_free	0.2510

fit	/app/data/saxs_computation/d0/1d0a/1d0a.fit
pddf	/app/data/pr_computation/d0/1d0a/1d0a.pr.out
profile	/app/data/saxs_computation/d0/1d0a/1d0a.dat

STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) IN COMPLEX WITH A HUMAN OX40 PEPTIDE

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

TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2

State in the Current Structure

Other States of the Same Protein in the Database

OX40L RECEPTOR PEPTIDE

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

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)