1czz

STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A 17-RESIDUE CD40 PEPTIDE

Method: X-RAY DIFFRACTION D_max: 80.4 Å Quality: EXCELLENT

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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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 315–501 Chain B； UniProt 315–501 Chain C； UniProt 315–501	Fragment：TRAF DOMAIN	CD 40 PEPTIDE × 2 （P25942）	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

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 1CZZ	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 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 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 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 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 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
1D01 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A HUMAN CD30 PEPTIDE Deposited 1999-09-07	Different construct 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 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 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 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 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 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
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 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 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 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 26 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 1–187； UniProt 315–501 Author chain B； PDBConstruct 1–187； UniProt 315–501 Author chain C； PDBConstruct 1–187； UniProt 315–501

CD 40 PEPTIDE

OrganismNot specified

UniProt P25942

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain D； UniProt 250–258 Chain E； UniProt 250–258	Fragment：TRAF2-BINDING REGION 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 5.6；293 K；PEG4K, MES, PH 5.6, VAPOR DIFFUSION, temperature 293K	Resolution 2.70 Å R-free 0.267

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1CZZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D00 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A 5-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 × 6 PDB declaration: hexameric	Chain I 250–254（5 aa） Fragment：ACETYLATED 5-RESIDUE PEPTIDE	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；pH 6；293 K；PEG4K, MES, Ph6.0, VAPOR DIFFUSION, temperature 20K	Resolution 2.00 Å R-free 0.254
1D00 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A 5-RESIDUE CD40 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 K 250–254（5 aa） Fragment：ACETYLATED 5-RESIDUE PEPTIDE Chain L 250–254（5 aa） Fragment：ACETYLATED 5-RESIDUE PEPTIDE Chain M 250–254（5 aa） Fragment：ACETYLATED 5-RESIDUE PEPTIDE	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；pH 6；293 K；PEG4K, MES, Ph6.0, VAPOR DIFFUSION, temperature 20K	Resolution 2.00 Å R-free 0.254
1D00 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A 5-RESIDUE CD40 PEPTIDE Deposited 1999-09-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain N 250–254（5 aa） Fragment：ACETYLATED 5-RESIDUE PEPTIDE Chain O 250–254（5 aa） Fragment：ACETYLATED 5-RESIDUE PEPTIDE Chain P 250–254（5 aa） Fragment：ACETYLATED 5-RESIDUE PEPTIDE	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；pH 6；293 K；PEG4K, MES, Ph6.0, VAPOR DIFFUSION, temperature 20K	Resolution 2.00 Å R-free 0.254
1D00 STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A 5-RESIDUE CD40 PEPTIDE Deposited 1999-09-07	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain J 250–254（5 aa） Fragment：ACETYLATED 5-RESIDUE PEPTIDE	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；pH 6；293 K；PEG4K, MES, Ph6.0, VAPOR DIFFUSION, temperature 20K	Resolution 2.00 Å R-free 0.254
1FLL MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3 Deposited 2000-08-14	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 X 246–266（21 aa） Fragment：CD40 (246-266) PEPTIDE	Mutation：N246K, C258S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å R-free 0.312
1FLL MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3 Deposited 2000-08-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 246–266（21 aa） Fragment：CD40 (246-266) PEPTIDE	Mutation：N246K, C258S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å R-free 0.312
1FLL MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3 Deposited 2000-08-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain Y 246–266（21 aa） Fragment：CD40 (246-266) PEPTIDE	Mutation：N246K, C258S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 3.50 Å R-free 0.312
1LB6 TRAF6-CD40 Complex Deposited 2002-04-02	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 230–238（9 aa） Fragment：residues 230-238	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG8000, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.258
3QD6 Crystal structure of the CD40 and CD154 (CD40L) complex Deposited 2011-01-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 21–190（170 aa） Fragment：extracellular domain Chain S 21–190（170 aa） Fragment：extracellular domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；12% PEG6000, 0.1M MOPS, 10% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.50 Å R-free 0.298
3QD6 Crystal structure of the CD40 and CD154 (CD40L) complex Deposited 2011-01-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain T 21–190（170 aa） Fragment：extracellular domain Chain U 21–190（170 aa） Fragment：extracellular domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；12% PEG6000, 0.1M MOPS, 10% isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.50 Å R-free 0.298
5DMI Structure of the extracellular domain of the CD40 in complex with CHI220 FAB Deposited 2015-09-08	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 23–193（171 aa） Fragment：Extracellular domain residues 23-193	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；80mM sodiym acetate, pH 4.6, 1.6 M ammonium sulfate, 20% (v/v) glycerol	Resolution 3.69 Å R-free 0.207
5DMJ Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB Deposited 2015-09-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–193（171 aa）	Mutation：D153, D180	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；293 K；100mM Citric Acid, pH 3.5, 20% (w/v) PEG 4000, 200 mM potassium formate	Resolution 2.79 Å R-free 0.258
5DMJ Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB Deposited 2015-09-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 23–193（171 aa）	Mutation：D153, D180	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；293 K；100mM Citric Acid, pH 3.5, 20% (w/v) PEG 4000, 200 mM potassium formate	Resolution 2.79 Å R-free 0.258
5DMJ Structure of the extracellular domain of the CD40 in complex with 3H56-5 DAB Deposited 2015-09-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 23–193（171 aa）	Mutation：D153, D180	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；293 K；100mM Citric Acid, pH 3.5, 20% (w/v) PEG 4000, 200 mM potassium formate	Resolution 2.79 Å R-free 0.258
5IHL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE CD40 IN COMPLEX WITH 3H56-5 DAB Deposited 2016-02-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 23–193（171 aa） Fragment：Extra Cellular Domain (UNP residues 23-193)	Mutation：Protein produced with Asn 153 & Asn 180, but deglycosylated with PNGase F, which leaves Asp at those positions	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；293 K；80mM Tris-HCl, pH 8.5, 1.6M Ammonium dihydrogen phosphate, 20% (v/v) Glycerol	Resolution 3.30 Å R-free 0.298
5IHL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE CD40 IN COMPLEX WITH 3H56-5 DAB Deposited 2016-02-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 23–193（171 aa） Fragment：Extra Cellular Domain (UNP residues 23-193)	Mutation：Protein produced with Asn 153 & Asn 180, but deglycosylated with PNGase F, which leaves Asp at those positions	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；293 K；80mM Tris-HCl, pH 8.5, 1.6M Ammonium dihydrogen phosphate, 20% (v/v) Glycerol	Resolution 3.30 Å R-free 0.298
5IHL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE CD40 IN COMPLEX WITH 3H56-5 DAB Deposited 2016-02-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 23–193（171 aa） Fragment：Extra Cellular Domain (UNP residues 23-193)	Mutation：Protein produced with Asn 153 & Asn 180, but deglycosylated with PNGase F, which leaves Asp at those positions	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；293 K；80mM Tris-HCl, pH 8.5, 1.6M Ammonium dihydrogen phosphate, 20% (v/v) Glycerol	Resolution 3.30 Å R-free 0.298
5IHL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE CD40 IN COMPLEX WITH 3H56-5 DAB Deposited 2016-02-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 23–193（171 aa） Fragment：Extra Cellular Domain (UNP residues 23-193)	Mutation：Protein produced with Asn 153 & Asn 180, but deglycosylated with PNGase F, which leaves Asp at those positions	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；293 K；80mM Tris-HCl, pH 8.5, 1.6M Ammonium dihydrogen phosphate, 20% (v/v) Glycerol	Resolution 3.30 Å R-free 0.298
6FAX Complex of Human CD40 Ectodomain with Lob 7.4 Fab Deposited 2017-12-18	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 21–193（173 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；NA X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；NA	Resolution 2.99 Å R-free 0.231
6PE8 Crystal structure of CD40/ABBV-323 FAB complex Deposited 2019-06-20	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 U 21–193（173 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；296.15 K；2M ammonium sulfate, 0.1M phosphate-citrate pH 4.2	Resolution 2.84 Å R-free 0.265
6PE8 Crystal structure of CD40/ABBV-323 FAB complex Deposited 2019-06-20	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 T 21–193（173 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；296.15 K；2M ammonium sulfate, 0.1M phosphate-citrate pH 4.2	Resolution 2.84 Å R-free 0.265
6PE9 Crystal Structure of CD40 complexed to FAB516 Deposited 2019-06-20	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 I 21–193（173 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；296.15 K；1.6M Ammonium Sulfate 2% w/v PEG1000, 100 mM HEPES Sodium Salt pH 7.5	Resolution 3.13 Å R-free 0.255
6PE9 Crystal Structure of CD40 complexed to FAB516 Deposited 2019-06-20	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 G 21–193（173 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；296.15 K；1.6M Ammonium Sulfate 2% w/v PEG1000, 100 mM HEPES Sodium Salt pH 7.5	Resolution 3.13 Å R-free 0.255
6PE9 Crystal Structure of CD40 complexed to FAB516 Deposited 2019-06-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain U 21–193（173 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；296.15 K；1.6M Ammonium Sulfate 2% w/v PEG1000, 100 mM HEPES Sodium Salt pH 7.5	Resolution 3.13 Å R-free 0.255
6PE9 Crystal Structure of CD40 complexed to FAB516 Deposited 2019-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain V 21–193（173 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；296.15 K；1.6M Ammonium Sulfate 2% w/v PEG1000, 100 mM HEPES Sodium Salt pH 7.5	Resolution 3.13 Å R-free 0.255
6PE9 Crystal Structure of CD40 complexed to FAB516 Deposited 2019-06-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 21–193（173 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；296.15 K；1.6M Ammonium Sulfate 2% w/v PEG1000, 100 mM HEPES Sodium Salt pH 7.5	Resolution 3.13 Å R-free 0.255
7P3I Crystal structure of human CD40/TNFRSF5 in complex with the anti-CD40 DARPin protein Deposited 2021-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–193（173 aa） Fragment：>FRAGMENT<	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；29.9999 %w/v PEG 4K, 0.24 M LiSO4, 0.0999 M TRIS, 0.35 M NaBr	Resolution 2.29 Å R-free 0.253
7P3I Crystal structure of human CD40/TNFRSF5 in complex with the anti-CD40 DARPin protein Deposited 2021-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 21–193（173 aa） Fragment：>FRAGMENT<	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；29.9999 %w/v PEG 4K, 0.24 M LiSO4, 0.0999 M TRIS, 0.35 M NaBr	Resolution 2.29 Å R-free 0.253
8YX1 CD40 in complex with Bleselumab Fab Deposited 2024-04-01	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 21–193（173 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium chloride 20% w/v Polyethylene glycol 3,350	Resolution 2.70 Å R-free 0.265
8YX1 CD40 in complex with Bleselumab Fab Deposited 2024-04-01	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 C 21–193（173 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium chloride 20% w/v Polyethylene glycol 3,350	Resolution 2.70 Å R-free 0.265
8YX9 CD40 in complex with Dacetuzumab Fab Deposited 2024-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 21–193（173 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium citrate tribasic pH 7.0 20% w/v Polyethylene glycol 3,350	Resolution 2.80 Å R-free 0.262
8YX9 CD40 in complex with Dacetuzumab Fab Deposited 2024-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 21–193（173 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium citrate tribasic pH 7.0 20% w/v Polyethylene glycol 3,350	Resolution 2.80 Å R-free 0.262
8YX9 CD40 in complex with Dacetuzumab Fab Deposited 2024-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 21–193（173 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium citrate tribasic pH 7.0 20% w/v Polyethylene glycol 3,350	Resolution 2.80 Å R-free 0.262
8YX9 CD40 in complex with Dacetuzumab Fab Deposited 2024-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 21–193（173 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium citrate tribasic pH 7.0 20% w/v Polyethylene glycol 3,350	Resolution 2.80 Å R-free 0.262

13 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TNR5_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 2–10； UniProt 250–258 Author chain E； PDBConstruct 2–10； UniProt 250–258

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	1czz
Deposition date deposition_date	1999-09-07
Structure title title	STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A 17-RESIDUE CD40 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	28.20 Å
Radius of gyration Rg (electron density) rg_electron	26.90 Å
Forward intensity I(0) i0	62103600.00
Molecular weight molecular_weight	61700.0 kDa
Excluded volume excluded_volume	77334 Å³
Envelope volume envelope_volume	96871 Å³
Hydration-shell volume shell_volume	30190 Å³
Envelope diameter envelope_diameter	79.5 Å
Shell Rg shell_rg	33.85 Å
Envelope Rg envelope_rg	26.65 Å
Shape Rg shape_rg	26.90 Å
Total Rg total_rg	27.63 Å
Total atoms total_atoms	4340
Residues n_residues	577
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	80.4 Å
Rg (real space) rg_real	27.98 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	6.2100e+07
I(0) uncertainty (real space) i0_real_error	8.8600e+05
Rg (reciprocal space) rg_reciprocal	28.05 Å
I(0) (reciprocal space) i0_reciprocal	62110000.0000
Solution quality estimate total_estimate	0.9171
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	37.3 Å
Skewness Skewness skewness	-0.005
Kurtosis Kurtosis kurtosis	-0.738
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5851000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.993; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.941

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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	21132.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4444

EALSSKVQQLERSIGLKDLAMADLEQKVLEMEASTYDGVFIWKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKMEAKNSYVRDDAIFIKAIVDLTGL

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	CD 40 PEPTIDE
Molecular weight formula_weight	1010.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E

XPVQETLHGC

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	104

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1czza1
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	d1czza2
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	d1czzb1
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	d1czzb2
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	d1czzc1
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	d1czzc2
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 (3 domains)

Domain ID domain_id	1czzA00
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	1czzB00
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	1czzC00
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	59.400 Å
Unit-cell length b length_b	81.100 Å
Unit-cell length c length_c	77.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2210
R_work r_work	0.2210
R_free r_free	0.2670

fit	/app/data/saxs_computation/cz/1czz/1czz.fit
pddf	/app/data/pr_computation/cz/1czz/1czz.pr.out
profile	/app/data/saxs_computation/cz/1czz/1czz.dat

STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A 17-RESIDUE CD40 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

CD 40 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) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)