SAXSdb — 1sm3

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

SM3 ANTIBODY

OrganismNot specified

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 L； UniProt 22–234	Fragment：FAB FRAGMENT	SM3 ANTIBODY × 1 （P01801） PEPTIDE EPITOPE × 1 （P15941） CD CADMIUM ION × 8 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 1.95 Å R-free 0.283

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 1SM3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1P4B Three-Dimensional Structure Of a Single Chain Fv Fragment Complexed With The peptide GCN4(7P-14P). Deposited 2003-04-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 22–117（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 4000, tris/HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293KK	Resolution 2.35 Å R-free 0.300
1P4I Crystal Structure of scFv against peptide GCN4 Deposited 2003-04-23	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 L 22–117（96 aa）	Mutation：N36S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；293 K；ammonium sulfate, sodium citrate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.260
1Q0X Anti-morphine Antibody 9B1 Unliganded Form Deposited 2003-07-17	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 L 22–117（96 aa）	Not recorded	SO4 SULFATE ION × 2 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；298 K；22% PEG MME 2000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 4.60	Resolution 1.60 Å R-free 0.251

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LV1A_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain L； PDBConstruct 3–215； UniProt 22–234

SM3 ANTIBODY

OrganismNot specified

UniProt P01801

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 H； UniProt 2–220	Fragment：FAB FRAGMENT	SM3 ANTIBODY × 1 （P01723） PEPTIDE EPITOPE × 1 （P15941） CD CADMIUM ION × 8 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 1.95 Å R-free 0.283

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 1SM3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2DLF HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 6.75 Deposited 1998-12-17	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 H 1–115（115 aa） Fragment：FV FRAGMENT (VH DOMAIN) SYNONYM: ANTI-DANSYL FV FRAGMENT	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.75；CRYSTALLIZATION CONDITIONS: TEMPERATURE AT 20C. PRECIPITANT SOLUTION CONTAINED 1 AMMONIUM SULFATE AND 0.025 M SODIUM CACODYLATE (PH 6.75). 5 MG/ML OF FV FRAGMENT., VAPOR DIFFUSION, HANGING DROP	Resolution 1.55 Å R-free 0.233
5A2I Crystal structure of scFv-SM3 in complex with APD-SGalNAc-RP Deposited 2015-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 6–115（110 aa） Fragment：RESIDUES 6-115,20-129	Not recorded	EDO 1,2-ETHANEDIOL × 2 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.88 Å R-free 0.261
5A2J Crystal structure of scFv-SM3 in complex with the naked peptide APDTRP Deposited 2015-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 6–115（110 aa） Fragment：RESIDUES 6-115,20-129	Not recorded	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.65 Å R-free 0.197
5A2K Crystal structure of scFv-SM3 in complex with APD-TGalNAc-RP Deposited 2015-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 6–115（110 aa） Fragment：RESIDUES 6-115,20-129	Not recorded	EDO 1,2-ETHANEDIOL × 6 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å R-free 0.216
5A2L Crystal structure of scFv-SM3 in complex with APD-CGalNAc-RP Deposited 2015-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 6–115（110 aa） Fragment：RESIDUES 6-115,20-129	Not recorded	EDO 1,2-ETHANEDIOL × 4 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.79 Å R-free 0.204
5N7B Understanding the singular conformational landscape of the Tn antigens: Sulfur-for- oxygen substitution in the glycosidic linkage provides new insights into molecular recognition by an antibody Deposited 2017-02-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–114（114 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 7 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350, 0.2 M disodium hydrogen phosphate	Resolution 1.70 Å R-free 0.211
5OWP Crystal structure of glycopeptide "GVTSAfPDT*RPAP" in complex with scFv-SM3 Deposited 2017-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 6–111（106 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PEG 3350, disodium hydrogen phosphate	Resolution 1.85 Å R-free 0.256

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

View Construct and Data Evidence

UniProt name	HV32_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 2–218； UniProt 2–220

PEPTIDE EPITOPE

OrganismNot specified

UniProt P15941

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 P； UniProt 139–151	Not recorded	SM3 ANTIBODY × 1 （P01723） SM3 ANTIBODY × 1 （P01801） CD CADMIUM ION × 8 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 1.95 Å R-free 0.283

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 1SM3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6BSB Crystal structure of the Mucin-1 SEA domain, L1105M mutant, Selenium-derivative Deposited 2017-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1041–1097（57 aa） Fragment：SEA domain, N-terminal Chain B 1098–1152（55 aa） Fragment：SEA domain, C-terminal	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 4.6；293 K；Native crystals (see related entry) were used as seeds in a drop of 1:1 mix of the SeMet-derivative (9 mg/ml in 10 mM Tris-Cl, pH 7.4) and reservoir solution (0.1 M sodium acetate trihydrate pH 4.6, 1.75 M sodium chloride, 0.2 M ammonium sulfate).	Resolution 1.60 Å R-free 0.222
6BSC Crystal structure of the Mucin-1 SEA domain Deposited 2017-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1041–1097（57 aa） Fragment：SEA domain, N-terminal Chain B 1098–1152（55 aa） Fragment：SEA domain, C-terminal	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；Drop was a 1:1 mix of protein (10 mg/ml in 10 mM Tris-Cl, pH 7.4) and reservoir solution (0.1 M sodium acetate trihydrate pH 4.6, 2.0 M sodium chloride)	Resolution 1.30 Å R-free 0.184
6FZQ Crystal structure of scFv-SM3 in complex with compound 3 Deposited 2018-03-15	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 P 141–146（6 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 10 EEN 2-deoxy-2-[(difluoroacetyl)amino]-alpha-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PEG 3350 disodium hydrogen phosphate	Resolution 1.70 Å R-free 0.225
6FZR Crystal structure of scFv-SM3 in complex with compound 2 Deposited 2018-03-15	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 P 141–146（6 aa） Fragment：UNP residues 141-146	Not recorded	EDO 1,2-ETHANEDIOL × 8 EEQ 2-deoxy-2-[(fluoroacetyl)amino]-alpha-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PEG 3350 disodium hydrogen phosphate	Resolution 1.80 Å R-free 0.232
6TGG scFv-1SM3 in complex with glycopeptide containing an sp2-imino sugar Deposited 2019-11-15	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 P 141–146（6 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4 N8W ~{N}-[(6~{S},7~{R},8~{S},8~{a}~{R})-7,8-bis(oxidanyl)-3-oxidanylidene-1,5,6,7,8,8~{a}-hexahydro-[1,3]oxazolo[3,4-a]pyridin-6-yl]ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PEG 3350 disodium hydrogen phosphate	Resolution 2.00 Å R-free 0.237
7Q4I Crystal structure of DmC1GalT1 in complex with UDP-Mn2+ and the APD-TGalNAc-RP Deposited 2021-10-31	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 F 141–146（6 aa） Chain G 141–146（6 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	UDP URIDINE-5'-DIPHOSPHATE × 2 EDO 1,2-ETHANEDIOL × 3 MN MANGANESE (II) ION × 2 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；potassium thiocyanate, Polyethylene glycol monomethyl ether 2,000	Resolution 2.40 Å R-free 0.235
7V4W Crystal structure of Antibody 16A in complex with MUC1 peptide Deposited 2021-08-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 145–157（13 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；Di-sodium hydrogen phosphate 0.2M, PEG 3350 20%	Resolution 2.10 Å R-free 0.233
7V64 Crystal structure of Antibody 16A in complex with MUC1 Glycopeptide(GlycoT) Deposited 2021-08-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 145–157（13 aa）	Not recorded	NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；1.0 M Lithium chloride, 0.1 M Tris pH 8.5, 20% PEG 6000	Resolution 1.56 Å R-free 0.203
7V7K Crystal structure of Antibody 16A in complex with MUC1 Glycopeptide(GlycoST) Deposited 2021-08-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 145–157（13 aa）	Not recorded	NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；1.0 M Lithium chloride, 0.1 M Tris pH 8.5, 20%(w/v) PEG 6000	Resolution 2.20 Å R-free 0.251
7V8Q Crystal structure of antibody 14A in complex with MUC1 Glycopeptide(GlycoT) Deposited 2021-08-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 145–157（13 aa）	Not recorded	NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；Crystal screen D4=JCSG F7, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 20% v/v 2-Propanol, 20% w/v Polyethylene glycol 4000	Resolution 3.20 Å R-free 0.244
7V8Q Crystal structure of antibody 14A in complex with MUC1 Glycopeptide(GlycoT) Deposited 2021-08-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 145–157（13 aa）	Not recorded	NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；Crystal screen D4=JCSG F7, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 20% v/v 2-Propanol, 20% w/v Polyethylene glycol 4000	Resolution 3.20 Å R-free 0.244
7V8Q Crystal structure of antibody 14A in complex with MUC1 Glycopeptide(GlycoT) Deposited 2021-08-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 145–157（13 aa）	Not recorded	NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；289 K；Crystal screen D4=JCSG F7, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 20% v/v 2-Propanol, 20% w/v Polyethylene glycol 4000	Resolution 3.20 Å R-free 0.244
7VAC Crystal structure of antibody 14A in complex with MUC1 glycopeptide(GlycoST) Deposited 2021-08-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 145–157（13 aa）	Not recorded	NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.1 M Sodium citrate pH 5.5, Isopropanol 10%, PEG 4000 20%	Resolution 3.50 Å R-free 0.219
7VAC Crystal structure of antibody 14A in complex with MUC1 glycopeptide(GlycoST) Deposited 2021-08-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 145–157（13 aa）	Not recorded	NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.1 M Sodium citrate pH 5.5, Isopropanol 10%, PEG 4000 20%	Resolution 3.50 Å R-free 0.219
7VAC Crystal structure of antibody 14A in complex with MUC1 glycopeptide(GlycoST) Deposited 2021-08-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 145–157（13 aa）	Not recorded	NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.1 M Sodium citrate pH 5.5, Isopropanol 10%, PEG 4000 20%	Resolution 3.50 Å R-free 0.219
7VAZ Crystal structure of antibody 14A in complex with MUC1 glycopeptide(GlycoS) Deposited 2021-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 145–157（13 aa）	Not recorded	NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.1 M Sodium citrate pH 5.5, Isopropanol 10%, PEG 4000 20%	Resolution 2.73 Å R-free 0.264
7VAZ Crystal structure of antibody 14A in complex with MUC1 glycopeptide(GlycoS) Deposited 2021-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 145–157（13 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.1 M Sodium citrate pH 5.5, Isopropanol 10%, PEG 4000 20%	Resolution 2.73 Å R-free 0.264
7VAZ Crystal structure of antibody 14A in complex with MUC1 glycopeptide(GlycoS) Deposited 2021-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 145–157（13 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.1 M Sodium citrate pH 5.5, Isopropanol 10%, PEG 4000 20%	Resolution 2.73 Å R-free 0.264
8AXH Crystal structure of a MUC1-like glycopeptide containing the unnatural L-4-hydroxynorvaline in complex with scFv-SM3 Deposited 2022-08-31	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 141–146（6 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 6 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；PEG 3350 disodium hydrogen phosphate	Resolution 1.85 Å R-free 0.206
8P6I Crystal structure of the 139H2 Fab fragment bound to Muc1 peptide epitope Deposited 2023-05-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 141–149（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；0.2M NaCl 20%w/v PEG 8K 0.1M Na Phos Cit pH 4.2	Resolution 2.50 Å R-free 0.254
8P6I Crystal structure of the 139H2 Fab fragment bound to Muc1 peptide epitope Deposited 2023-05-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain a 141–149（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；0.2M NaCl 20%w/v PEG 8K 0.1M Na Phos Cit pH 4.2	Resolution 2.50 Å R-free 0.254
8S6K Crystal structure of ScFv-G2D11 complexed to a bis-Tn glycopeptide Deposited 2024-02-27	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 M 127–133（7 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 7 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；lithium chloride Tris PEG 8000	Resolution 1.75 Å R-free 0.221
8S6K Crystal structure of ScFv-G2D11 complexed to a bis-Tn glycopeptide Deposited 2024-02-27	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 N 127–133（7 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 5 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；lithium chloride Tris PEG 8000	Resolution 1.75 Å R-free 0.221
8S6T Crystal structure of Fab-3F1 complexed to a bis-STn glycopeptide Deposited 2024-02-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 126–138（13 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Magnesium chloride hexahydrate calcium chloride dihydrate NDSB sodium HEPES MOPS ethylene glycol PEG 8000	Resolution 1.85 Å R-free 0.267
8S6V Crystal structure of Fab-2D9 chimera complexed to a bis-Tn glycopeptide Deposited 2024-02-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 127–135（9 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 4 SO4 SULFATE ION × 2 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；lithium sulfate Bis-Tris PEG 3350	Resolution 1.95 Å R-free 0.244
8S6V Crystal structure of Fab-2D9 chimera complexed to a bis-Tn glycopeptide Deposited 2024-02-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain N 127–135（9 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 7 SO4 SULFATE ION × 3 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；lithium sulfate Bis-Tris PEG 3350	Resolution 1.95 Å R-free 0.244

17 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MUC1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain P； PDBConstruct 1–13； UniProt 139–151

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1sm3
Deposition date deposition_date	1997-12-23
Structure title title	CRYSTAL STRUCTURE OF THE TUMOR SPECIFIC ANTIBODY SM3 COMPLEX WITH ITS PEPTIDE EPITOPE
Keywords keywords	ANTIBODY, PEPTIDE ANTIGEN, ANTITUMOR ANTIBODY, COMPLEX (ANTIBODY-PEPTIDE EPITOPE), COMPLEX (ANTIBODY-PEPTIDE EPITOPE) complex; COMPLEX (ANTIBODY/PEPTIDE EPITOPE)
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	25.05 Å
Radius of gyration Rg (electron density) rg_electron	23.98 Å
Forward intensity I(0) i0	38981100.00
Molecular weight molecular_weight	46731.0 kDa
Excluded volume excluded_volume	57478 Å³
Envelope volume envelope_volume	69197 Å³
Hydration-shell volume shell_volume	24349 Å³
Envelope diameter envelope_diameter	80.7 Å
Shell Rg shell_rg	30.78 Å
Envelope Rg envelope_rg	23.66 Å
Shape Rg shape_rg	23.90 Å
Total Rg total_rg	24.96 Å
Total atoms total_atoms	3233
Residues n_residues	420
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	78.5 Å
Rg (real space) rg_real	25.02 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	3.8980e+07
I(0) uncertainty (real space) i0_real_error	5.2230e+05
Rg (reciprocal space) rg_reciprocal	25.03 Å
I(0) (reciprocal space) i0_reciprocal	38980000.0000
Solution quality estimate total_estimate	0.9101
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.266
Kurtosis Kurtosis kurtosis	-0.513
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5733000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.971

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	SM3 ANTIBODY
Molecular weight formula_weight	23149.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	3564

DIVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLGSEKSSPSVTLFPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSYLTLTARAWERHSSYSCQVTHEGHTVEKSLSRADCS

Entity 2 Entity 2 polymer

Description description	SM3 ANTIBODY
Molecular weight formula_weight	23460.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLQESGGGLVQPGGSMKLSCVASGFTFSNYWMNWVRQSPEKGLEWVAEIRLKSNNYATHYAESVKGRFTISRDDSKSSVYLQMNNLRAEDTGIYYCTGVGQFAYWGQGTTVTVSSAKTTPPTVYPLAPGSNAASQSMVTLGCLVKGYFPEPVTVTWNSGSLASGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDAKIVPRD

Entity 3 Entity 3 polymer

Description description	PEPTIDE EPITOPE
Molecular weight formula_weight	1258.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

TSAPDTRPAPGST

Entity 4 Entity 4 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	331

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1sm3h1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1sm3h2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1sm3h3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1sm3l1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1sm3l2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (4 domains)

Domain ID domain_id	1sm3H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1sm3H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1sm3L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1sm3L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (2)

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Unit-cell length a length_a	42.200 Å
Unit-cell length b length_b	83.730 Å
Unit-cell length c length_c	67.240 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2130
R_work r_work	0.2130
R_free r_free	0.2830

fit	/app/data/saxs_computation/sm/1sm3/1sm3.fit
pddf	/app/data/pr_computation/sm/1sm3/1sm3.pr.out
profile	/app/data/saxs_computation/sm/1sm3/1sm3.dat

CRYSTAL STRUCTURE OF THE TUMOR SPECIFIC ANTIBODY SM3 COMPLEX WITH ITS PEPTIDE EPITOPE

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

SM3 ANTIBODY

State in the Current Structure

Other States of the Same Protein in the Database

SM3 ANTIBODY

State in the Current Structure

Other States of the Same Protein in the Database

PEPTIDE EPITOPE

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)