Current Protein Identity:P25942 New Search
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
1CZZ STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A 17-RESIDUE CD40 PEPTIDE Deposited 1999-09-07 Assembly 1 Protein heterocomplex Heteromer;Protein × 5 PDB declaration: pentameric(5) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 6 PDB declaration: hexameric(6) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 6 PDB declaration: hexameric(6) Consistent with protein count
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 Assembly 3 Protein heterocomplex Heteromer;Protein × 6 PDB declaration: hexameric(6) Consistent with protein count
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 Assembly 4 Protein heterocomplex Heteromer;Protein × 6 PDB declaration: hexameric(6) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 3 Protein heterocomplex Heteromer;Protein × 6 PDB declaration: hexameric(6) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 5 PDB declaration: pentameric(5) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 5 PDB declaration: pentameric(5) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 3 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 3 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 4 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 3 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 4 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 5 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 3 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 4 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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