8yx9

CD40 in complex with Dacetuzumab Fab

Method: X-RAY DIFFRACTION D_max: 227.3 Å Quality: GOOD

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

Tumor necrosis factor receptor superfamily member 5

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 21–193	Not recorded	Dacetuzumab, Heavy chain × 1 Dacetuzumab, light chain × 1 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain J； UniProt 21–193	Not recorded	Dacetuzumab, Heavy chain × 1 Dacetuzumab, light chain × 1 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
3	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 21–193	Not recorded	Dacetuzumab, Heavy chain × 1 Dacetuzumab, light chain × 1 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
4	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain K； UniProt 21–193	Not recorded	Dacetuzumab, Heavy chain × 1 Dacetuzumab, light chain × 1 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

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 8YX9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 250–258（9 aa） Fragment：TRAF2-BINDING REGION Chain E 250–258（9 aa） Fragment：TRAF2-BINDING REGION	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 5.6；293 K；PEG4K, MES, PH 5.6, VAPOR DIFFUSION, temperature 293K	Resolution 2.70 Å R-free 0.267
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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state 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 oligomeric state 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 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 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） 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 ligand/ion 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 ligand/ion 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 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 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 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 ligand/ion 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 ligand/ion 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 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 ligand/ion 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 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 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 ligand/ion 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 ligand/ion 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

13 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TNR5_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–173； UniProt 21–193 Author chain D； PDBConstruct 1–173； UniProt 21–193 Author chain J； PDBConstruct 1–173； UniProt 21–193 Author chain K； PDBConstruct 1–173； UniProt 21–193

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	8yx9
Deposition date deposition_date	2024-04-02
Structure title title	CD40 in complex with Dacetuzumab Fab
Keywords keywords	CD40, Dacetuzumab, Bleselumab, agonist activity, tumor necrosis factor, IMMUNE SYSTEM; IMMUNE SYSTEM
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	60.43 Å
Radius of gyration Rg (electron density) rg_electron	61.80 Å
Forward intensity I(0) i0	889391000.00
Molecular weight molecular_weight	239390.0 kDa
Excluded volume excluded_volume	296330 Å³
Envelope volume envelope_volume	494360 Å³
Hydration-shell volume shell_volume	77635 Å³
Envelope diameter envelope_diameter	308.2 Å
Shell Rg shell_rg	51.18 Å
Envelope Rg envelope_rg	65.92 Å
Shape Rg shape_rg	61.71 Å
Total Rg total_rg	61.74 Å
Total atoms total_atoms	16810
Residues n_residues	2199
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	227.3 Å
Rg (real space) rg_real	61.17 Å
Rg uncertainty (real space) rg_real_error	2.79 Å
I(0) (real space) i0_real	8.8660e+08
I(0) uncertainty (real space) i0_real_error	1.8940e+07
Rg (reciprocal space) rg_reciprocal	59.06 Å
I(0) (reciprocal space) i0_reciprocal	885000000.0000
Solution quality estimate total_estimate	0.7779
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	61.2 Å
Skewness Skewness skewness	0.904
Kurtosis Kurtosis kurtosis	0.601
Angular range angular_range	— – 0.1300 Å⁻¹
Current regularization parameter α current_alpha	0.0154
Highest regularization parameter α highest_alpha	42290000.0000
Real-space data points n_real_points	27
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 0.426; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.893

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Dacetuzumab, Heavy chain
Molecular weight formula_weight	23858.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,B,E,G
Atom count atom_count	16889

EVQLVESGGGLVQPGGSLRLSCAASGYSFTGYYIHWVRQAPGKGLEWVARVIPNAGGTSYNQKFKGRFTLSVDNSKNTAYLQMNSLRAEDTAVYYCAREGIYWWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCHHHHHH

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Dacetuzumab, light chain
Molecular weight formula_weight	24025.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,C,F,I

DIQMTQSPSSLSASVGDRVTITCRSSQSLVHSNGNTFLHWYQQKPGKAPKLLIYTVSNRFSGVPSRFSGSGSGTDFTLTISSLQPEDFATYFCSQTTHVPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Tumor necrosis factor receptor superfamily member 5
Molecular weight formula_weight	20016.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,J,K

EPPTACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQHKYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSDTICEPCPVGFFSNVSSAFEKCHPWTSCETKDLVVQQAGTNKTDVVCGPQDRLRHHHHHH

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	Homo sapiens

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	58

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8. Citations (1)

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Unit-cell length a length_a	199.194 Å
Unit-cell length b length_b	208.172 Å
Unit-cell length c length_c	198.061 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	49.800 Å
R factor r_factor	—
R_work r_work	0.2090
R_free r_free	0.2617

fit	/app/data/saxs_computation/yx/8yx9/8yx9.fit
pddf	/app/data/pr_computation/yx/8yx9/8yx9.pr.out
profile	/app/data/saxs_computation/yx/8yx9/8yx9.dat

CD40 in complex with Dacetuzumab Fab

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

Tumor necrosis factor receptor superfamily member 5

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)