3qd6

Crystal structure of the CD40 and CD154 (CD40L) complex

Method: X-RAY DIFFRACTION D_max: 148.9 Å Quality: GOOD

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

CD40 ligand

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 116–261 Chain B； UniProt 116–261 Chain C； UniProt 116–261	Fragment：secreted form, soluble form	Tumor necrosis factor receptor superfamily member 5 × 2 （P25942） 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
2	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain D； UniProt 116–261 Chain E； UniProt 116–261 Chain F； UniProt 116–261	Fragment：secreted form, soluble form	Tumor necrosis factor receptor superfamily member 5 × 2 （P25942） 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

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 3QD6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ALY CRYSTAL STRUCTURE OF HUMAN CD40 LIGAND Deposited 1997-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 116–261（146 aa） Fragment：EXTRACELLULAR DOMAIN FRAGMENT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 1.4 M NA CITRATE, 50 MM HEPES PH 7.5	Resolution 2.00 Å R-free 0.295
1I9R STRUCTURE OF CD40L IN COMPLEX WITH THE FAB FRAGMENT OF HUMANIZED 5C8 ANTIBODY Deposited 2001-03-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 116–261（146 aa） Fragment：RESIDUES 116-261 Chain B 116–261（146 aa） Fragment：RESIDUES 116-261 Chain C 116–261（146 aa） Fragment：RESIDUES 116-261	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20% PEG MME 550, 0.1 M MES, 0.01 M zinc sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.285
3LKJ Small Molecule Inhibition of the TNF Family Cyokine CD40 Ligand Through a Subunit Fracture Mechanism Deposited 2010-01-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 121–261（141 aa） Fragment：UNP residues 121-261 Chain B 121–261（141 aa） Fragment：UNP residues 121-261 Chain C 121–261（141 aa） Fragment：UNP residues 121-261	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 LKJ (2R)-{[(2'-[(biphenyl-3-ylmethyl)carbamoyl]-6'-{[(2R)-2-(pyrrolidin-1-ylmethyl)pyrrolidin-1-yl]carbonyl}-6-{[(2R)-2-(1H-pyrrol-1-ylmethyl)pyrrolidin-1-yl]carbonyl}-4,4'-bipyridin-2-yl)carbonyl]amino}(cyclohexyl)ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；24% Peg3350, 50mM Hepes pH 7.5, 0.2M Sodium Citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.305
6BRB Novel non-antibody protein scaffold targeting CD40L Deposited 2017-11-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 120–261（142 aa） Fragment：UNP residues 120-261	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；40% v/v PEG600, 0.1 M sodium acetate, 0.2 M magnesium chloride	Resolution 2.82 Å R-free 0.273
6W9G Crystal Structure of the Fab fragment of humanized 5c8 antibody containing the fluorescent non-canonical amino acid L-(7-hydroxycoumarin-4-yl)ethylglycine in complex with CD40L at pH 6.8 Deposited 2020-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 116–261（146 aa） Chain B 116–261（146 aa） Chain C 116–261（146 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 8 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 TMO trimethylamine oxide × 21 ETE 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 3 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；20% PEG MME 2000, 0.1 M Trimethylamine N-oxide, 0.1 M Tris-HCl pH 7.5	Resolution 1.82 Å R-free 0.207
7SGM Crystal structure of a Fab variant containing a fluorescent noncanonical amino acid with blocked excited state proton transfer and in complex with its antigen, CD40L Deposited 2021-10-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 116–261（146 aa） Chain B 116–261（146 aa） Chain C 116–261（146 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 13 TMO trimethylamine oxide × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；16-24% PEG MME 2000, 0.1 M Trimethylamine N-oxide, 0.1 M Tris-HCl pH 7.5-9.0	Resolution 2.00 Å R-free 0.228
9I5N Single particle cryo electron microscopy of a Fab fragment bound to recombinant human CD40 ligand Deposited 2025-01-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 119–261（143 aa）	Not recorded	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

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

View Construct and Data Evidence

UniProt name	CD40L_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–149； UniProt 116–261 Author chain B； PDBConstruct 4–149； UniProt 116–261 Author chain C； PDBConstruct 4–149； UniProt 116–261 Author chain D； PDBConstruct 4–149； UniProt 116–261 Author chain E； PDBConstruct 4–149； UniProt 116–261 Author chain F； PDBConstruct 4–149； UniProt 116–261

Tumor necrosis factor receptor superfamily member 5

Homo sapiens

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 R； UniProt 21–190 Chain S； UniProt 21–190	Fragment：extracellular domain	CD40 ligand × 3 （P29965） 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
2	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain T； UniProt 21–190 Chain U； UniProt 21–190	Fragment：extracellular domain	CD40 ligand × 3 （P29965） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3QD6	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 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 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 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
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 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 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 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 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 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 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 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 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 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 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 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 33 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 R； PDBConstruct 1–170； UniProt 21–190 Author chain S； PDBConstruct 1–170； UniProt 21–190 Author chain T； PDBConstruct 1–170； UniProt 21–190 Author chain U； PDBConstruct 1–170； UniProt 21–190

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	3qd6
Deposition date deposition_date	2011-01-18
Structure title title	Crystal structure of the CD40 and CD154 (CD40L) complex
Keywords keywords	Immune regulator, receptor, CYTOKINE-CYTOKINE RECEPTOR complex; CYTOKINE/CYTOKINE RECEPTOR
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	39.54 Å
Radius of gyration Rg (electron density) rg_electron	39.23 Å
Forward intensity I(0) i0	324825000.00
Molecular weight molecular_weight	141490.0 kDa
Excluded volume excluded_volume	174940 Å³
Envelope volume envelope_volume	236070 Å³
Hydration-shell volume shell_volume	51196 Å³
Envelope diameter envelope_diameter	162.6 Å
Shell Rg shell_rg	43.10 Å
Envelope Rg envelope_rg	40.38 Å
Shape Rg shape_rg	39.15 Å
Total Rg total_rg	39.68 Å
Total atoms total_atoms	9896
Residues n_residues	1276
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	148.9 Å
Rg (real space) rg_real	39.91 Å
Rg uncertainty (real space) rg_real_error	1.76 Å
I(0) (real space) i0_real	3.2480e+08
I(0) uncertainty (real space) i0_real_error	5.9550e+06
Rg (reciprocal space) rg_reciprocal	39.68 Å
I(0) (reciprocal space) i0_reciprocal	324700000.0000
Solution quality estimate total_estimate	0.8072
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.2 Å
Skewness Skewness skewness	0.577
Kurtosis Kurtosis kurtosis	-0.059
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	48580000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.588; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.749; Smooth: 0.977

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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	CD40 ligand
Molecular weight formula_weight	16096.1 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	9896

ADPGDQNPQIAAHVISEASSKTTSVLQWAEKGYYTMSNNLVTLENGKQLTVKRQGLYYIYAQVTFCSNREASSQAPFIASLCLKSPGRFERILLRAANTHSSAKPCGQQSIHLGGVFELQPGASVFVNVTDPSQVSHGTGFTSFGLLKL

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Tumor necrosis factor receptor superfamily member 5
Molecular weight formula_weight	19527.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R,S,T,U

EPPTACREKQYLINSQCCSLCQPGQKLVSDCTEFTETECLPCGESEFLDTWNRETHCHQHKYCDPNLGLRVQQKGTSETDTICTCEEGWHCTSEACESCVLHRSCSPGFGVKQIATGVSDTICEPCPVGFFSNVSSAFEKCHPWTSCETKDLVVQQAGTNKTDVVCGPQDSGRLVPR

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	Trichoplusia ni

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	6

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7. Fold Classification (SCOP + CATH) 14 domains

CATH v4.4 (14 domains)

Domain ID domain_id	3qd6A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3qd6B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3qd6C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3qd6D00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3qd6E00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3qd6F00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3qd6R01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	3qd6R02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	3qd6S01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	3qd6S02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	3qd6T01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	3qd6T02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	3qd6U01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	3qd6U02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

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8. Citations (1)

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Unit-cell length a length_a	133.212 Å
Unit-cell length b length_b	133.212 Å
Unit-cell length c length_c	211.151 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	114.961 Å
R factor r_factor	0.2450
R_work r_work	0.2450
R_free r_free	0.2980

fit	/app/data/saxs_computation/qd/3qd6/3qd6.fit
pddf	/app/data/pr_computation/qd/3qd6/3qd6.pr.out
profile	/app/data/saxs_computation/qd/3qd6/3qd6.dat

Crystal structure of the CD40 and CD154 (CD40L) complex

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

CD40 ligand

State in the Current Structure

Other States of the Same Protein in the Database

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 14 domains

CATH v4.4 (14 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)