1plg

EVIDENCE FOR THE EXTENDED HELICAL NATURE OF POLYSACCHARIDE EPITOPES. THE 2.8 ANGSTROMS RESOLUTION STRUCTURE AND THERMODYNAMICS OF LIGAND BINDING OF AN ANTIGEN BINDING FRAGMENT SPECIFIC FOR ALPHA-(2->8)-POLYSIALIC ACID

Method: X-RAY DIFFRACTION D_max: 76.9 Å Quality: EXCELLENT

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

IGG2A=KAPPA=

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 1–98	Fragment：FAB FRAGMENT THAT BINDS POLYSIALIC ACID	IGG2A=KAPPA= × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.80 Å

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 1PLG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AXT IMMUNE VERSUS NATURAL SELECTION: ANTIBODY ALDOLASES WITH THE RATES OF NATURAL ENZYMES Deposited 1997-10-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–100（100 aa） Fragment：;FAB' FRAGMENT 33F12 ;	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；PROTEIN WAS CRYSTALLIZED FROM 18% PEG 4000, 10% ISOPROPANOL, 100 MM HEPES, PH 7.4.	Resolution 2.15 Å R-free 0.317
1EGJ DOMAIN 4 OF THE BETA COMMON CHAIN IN COMPLEX WITH AN ANTIBODY Deposited 2000-02-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1–220（220 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；12% peg 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K	Resolution 2.80 Å R-free 0.288
1FLR 4-4-20 FAB FRAGMENT Deposited 1995-01-19	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–101（101 aa）	Not recorded	FLU 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.85 Å
1FPT THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN THE FAB FRAGMENT OF AN NEUTRALIZING ANTIBODY FOR TYPE 1 POLIOVIRUS AND ITS VIRAL EPITOPE Deposited 1995-01-26	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1–100（100 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
1GGB MAJOR ANTIGEN-INDUCED DOMAIN REARRANGEMENTS IN AN ANTIBODY Deposited 1993-07-19	Different construct	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–100（100 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1GGC MAJOR ANTIGEN-INDUCED DOMAIN REARRANGEMENTS IN AN ANTIBODY Deposited 1993-07-19	Different construct	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–100（100 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1KB5 MURINE T-CELL RECEPTOR VARIABLE DOMAIN/FAB COMPLEX Deposited 1997-04-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 1–99（99 aa） Fragment：FAB	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；15% PEG6000, 100MM HEPES PH 6.9-7.5, 200MM NACL, 0.1% NAN3, pH 7.2	Resolution 2.50 Å
1LO0 Catalytic Retro-Diels-Alderase Transition State Analogue Complex Deposited 2002-05-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 1–101（101 aa）	Not recorded	BC1 3-{[(9-CYANO-9,10-DIHYDRO-10-METHYLACRIDIN-9-YL)CARBONYL]AMINO}PROPANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；PEG, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.00 Å R-free 0.255
1LO0 Catalytic Retro-Diels-Alderase Transition State Analogue Complex Deposited 2002-05-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–101（101 aa）	Not recorded	BC1 3-{[(9-CYANO-9,10-DIHYDRO-10-METHYLACRIDIN-9-YL)CARBONYL]AMINO}PROPANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；PEG, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.00 Å R-free 0.255
1NBY Crystal Structure of HyHEL-63 complexed with HEL mutant K96A Deposited 2002-12-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；PEG 4000, AMMONIUM ACETATE, SODIUM ACETATE, pH 4.60, VAPOR DIFFUSION, HANGING DROP	Resolution 1.80 Å R-free 0.250
1NBZ Crystal Structure of HyHEL-63 complexed with HEL mutant K97A Deposited 2002-12-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；PEG 4000, AMMONIUM ACETATE, SODIUM ACETATE, pH 4.60, VAPOR DIFFUSION, HANGING DROP	Resolution 1.85 Å R-free 0.229
1NCA REFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE-NC41 FAB COMPLEX Deposited 1992-01-21	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain H 1–101（101 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CA CALCIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1NCA REFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE-NC41 FAB COMPLEX Deposited 1992-01-21	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 20 PDB declaration: eicosameric	Chain H 1–101（101 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 CA CALCIUM ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1NCB CRYSTAL STRUCTURES OF TWO MUTANT NEURAMINIDASE-ANTIBODY COMPLEXES WITH AMINO ACID SUBSTITUTIONS IN THE INTERFACE Deposited 1992-01-21	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain H 1–101（101 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1NCB CRYSTAL STRUCTURES OF TWO MUTANT NEURAMINIDASE-ANTIBODY COMPLEXES WITH AMINO ACID SUBSTITUTIONS IN THE INTERFACE Deposited 1992-01-21	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 20 PDB declaration: eicosameric	Chain H 1–101（101 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CA CALCIUM ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1NCC CRYSTAL STRUCTURES OF TWO MUTANT NEURAMINIDASE-ANTIBODY COMPLEXES WITH AMINO ACID SUBSTITUTIONS IN THE INTERFACE Deposited 1992-01-21	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain H 1–101（101 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CA CALCIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1NCD REFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE-NC41 FAB COMPLEX Deposited 1992-01-21	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain H 1–101（101 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å
1ND0 CATIONIC CYCLIZATION ANTIBODY 4C6 COMPLEX WITH TRANSITION STATE ANALOG Deposited 2002-12-05	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 B 1–102（102 aa） Fragment：IMMUNOGLOBULIN FAB FRAGMENT, heavy chain Chain D 1–102（102 aa） Fragment：IMMUNOGLOBULIN FAB FRAGMENT, heavy chain	Not recorded	DP4 (1s,4s)-4-[dimethyl(phenyl)silyl]-1-methylpiperidine 1-oxide × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；295 K；ammonium sulfate, dioxane, tri-sodium citrate dihydrate, pH 5.5, evaporation, temperature 295K	Resolution 2.45 Å R-free 0.286
1ND0 CATIONIC CYCLIZATION ANTIBODY 4C6 COMPLEX WITH TRANSITION STATE ANALOG Deposited 2002-12-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–102（102 aa） Fragment：IMMUNOGLOBULIN FAB FRAGMENT, heavy chain Chain H 1–102（102 aa） Fragment：IMMUNOGLOBULIN FAB FRAGMENT, heavy chain	Not recorded	DP4 (1s,4s)-4-[dimethyl(phenyl)silyl]-1-methylpiperidine 1-oxide × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；295 K；ammonium sulfate, dioxane, tri-sodium citrate dihydrate, pH 5.5, evaporation, temperature 295K	Resolution 2.45 Å R-free 0.286
1ND0 CATIONIC CYCLIZATION ANTIBODY 4C6 COMPLEX WITH TRANSITION STATE ANALOG Deposited 2002-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–102（102 aa） Fragment：IMMUNOGLOBULIN FAB FRAGMENT, heavy chain	Not recorded	DP4 (1s,4s)-4-[dimethyl(phenyl)silyl]-1-methylpiperidine 1-oxide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；295 K；ammonium sulfate, dioxane, tri-sodium citrate dihydrate, pH 5.5, evaporation, temperature 295K	Resolution 2.45 Å R-free 0.286
1ND0 CATIONIC CYCLIZATION ANTIBODY 4C6 COMPLEX WITH TRANSITION STATE ANALOG Deposited 2002-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–102（102 aa） Fragment：IMMUNOGLOBULIN FAB FRAGMENT, heavy chain	Not recorded	DP4 (1s,4s)-4-[dimethyl(phenyl)silyl]-1-methylpiperidine 1-oxide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；295 K；ammonium sulfate, dioxane, tri-sodium citrate dihydrate, pH 5.5, evaporation, temperature 295K	Resolution 2.45 Å R-free 0.286
1ND0 CATIONIC CYCLIZATION ANTIBODY 4C6 COMPLEX WITH TRANSITION STATE ANALOG Deposited 2002-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–102（102 aa） Fragment：IMMUNOGLOBULIN FAB FRAGMENT, heavy chain	Not recorded	DP4 (1s,4s)-4-[dimethyl(phenyl)silyl]-1-methylpiperidine 1-oxide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；295 K；ammonium sulfate, dioxane, tri-sodium citrate dihydrate, pH 5.5, evaporation, temperature 295K	Resolution 2.45 Å R-free 0.286
1ND0 CATIONIC CYCLIZATION ANTIBODY 4C6 COMPLEX WITH TRANSITION STATE ANALOG Deposited 2002-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–102（102 aa） Fragment：IMMUNOGLOBULIN FAB FRAGMENT, heavy chain	Not recorded	DP4 (1s,4s)-4-[dimethyl(phenyl)silyl]-1-methylpiperidine 1-oxide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；295 K；ammonium sulfate, dioxane, tri-sodium citrate dihydrate, pH 5.5, evaporation, temperature 295K	Resolution 2.45 Å R-free 0.286
1NDG Crystal structure of Fab fragment of antibody HyHEL-8 complexed with its antigen lysozyme Deposited 2002-12-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–96（96 aa）	Not recorded	ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 1.90 Å R-free 0.249
1NDM Crystal structure of Fab fragment of antibody HyHEL-26 complexed with lysozyme Deposited 2002-12-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–96（96 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 2.10 Å R-free 0.258
1ORQ X-ray structure of a voltage-dependent potassium channel in complex with an Fab Deposited 2003-03-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 1–99（99 aa）	Not recorded	CD CADMIUM ION × 28 K POTASSIUM ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；PEG400, Cadmium chloride, Sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.20 Å R-free 0.298
1ORQ X-ray structure of a voltage-dependent potassium channel in complex with an Fab Deposited 2003-03-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain B 1–99（99 aa）	Not recorded	CD CADMIUM ION × 56 K POTASSIUM ION × 48	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；PEG400, Cadmium chloride, Sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.20 Å R-free 0.298
1RU9 Crystal Structure (A) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 4.6 with a data set collected in-house. Deposited 2003-12-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–102（102 aa） Fragment：fab	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 5 ACT ACETATE ION × 1 BEZ BENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；295 K；0.1M sodium acetate, pH 4.6, 0.2 M ammonium acetate, 15% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.50 Å R-free 0.247
1RUA Crystal structure (B) of u.v.-irradiated cationic cyclization antibody 4C6 fab at pH 4.6 with a data set collected at SSRL beamline 11-1. Deposited 2003-12-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–102（102 aa） Fragment：fab	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 1 GOL GLYCEROL × 3 BEZ BENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；295 K；0.1M sodium acetate, 0.2 M ammonium acetate, 15% (w/v) PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.75 Å R-free 0.251
1RUK Crystal structure (C) of native cationic cyclization antibody 4C6 fab at pH 4.6 with a data set collected at SSRL beamline 9-1 Deposited 2003-12-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–102（102 aa） Fragment：fab	Not recorded	ACT ACETATE ION × 1 BEZ BENZOIC ACID × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；295 K；0.1M sodium acetate, 0.2 M ammonium acetate, 15% (w/v) PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.40 Å R-free 0.210
1RUL Crystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6 with a data set collected at SSRL beamline 11-1. Deposited 2003-12-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–102（102 aa） Fragment：fab	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 1 GOL GLYCEROL × 4 BEZ BENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；295 K；0.1 M tri-sodium citrate, 0.2M ammonium acetate, 15% (w/v) PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.88 Å R-free 0.283
1RUM Crystal structure (F) of H2O2-soaked cationic cyclization antibody 4C6 fab at pH 8.5 with a data set collected at SSRL beamline 9-1. Deposited 2003-12-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–102（102 aa） Fragment：fab	Not recorded	BEZ BENZOIC ACID × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.1 M tris hydrochloride, pH 8.5, 0.2 M sodium acetate, 15% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.48 Å R-free 0.245
1RUP Crystal structure (G) of native cationic cyclization antibody 4C6 fab at pH 8.5 with a data set collected at APS beamline 19-ID Deposited 2003-12-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–102（102 aa） Fragment：fab	Not recorded	BEZ BENZOIC ACID × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.1 M tris hydrochloride, 0.2 M sodium acetate, 15% (w/v) PEG 4000 , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.40 Å R-free 0.212
1YEE STRUCTURE OF A CATALYTIC ANTIBODY, IGG2A FAB FRAGMENT (D2.5) Deposited 1997-04-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	PNB 4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 2.20 Å R-free 0.260
4FAB THREE-DIMENSIONAL STRUCTURE OF A FLUORESCEIN-FAB COMPLEX CRYSTALLIZED IN 2-METHYL-2,4-PENTANEDIOL Deposited 1989-04-10	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–98（98 aa）	Not recorded	FLU 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å
4ZXB Structure of the human insulin receptor ectodomain, IRDeltabeta construct, in complex with four Fab molecules Deposited 2015-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain C 7–106（100 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Crystals were produced by vapour diffusion using 1 microlitre of the complex (2.6 mg/ml) in 10 mM HEPES (pH 7.5), 0.02% sodium azide and 10% D-trehalose solution and 1 microlitres of well solution containing 10% PEG 8000, 0.1 M MES (pH 6.5) and 0.1 M MgAc2.	Resolution 3.30 Å R-free 0.237
6UQC Mouse IgG2a Bispecific Fc Deposited 2019-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 119–325（207 aa） Chain E 119–325（207 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FUC alpha-L-fucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；295.15 K；21% PEG10000 and 0.1M bicine pH 7.9	Resolution 1.87 Å R-free 0.229
6UQC Mouse IgG2a Bispecific Fc Deposited 2019-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 119–325（207 aa） Chain F 119–325（207 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FUC alpha-L-fucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；295.15 K；21% PEG10000 and 0.1M bicine pH 7.9	Resolution 1.87 Å R-free 0.229
8AQT Beta SARS-CoV-2 Spike bound to mouse ACE2 (local) Deposited 2022-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 97–328（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
8AQU BA.1 SARS-CoV-2 Spike bound to mouse ACE2 (local) Deposited 2022-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 97–328（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
8AQV BA.2.12.1 SARS-CoV-2 Spike bound to mouse ACE2 (local) Deposited 2022-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 97–328（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å

31 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GCAM_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 118–215； UniProt 1–98

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	1plg
Deposition date deposition_date	1995-04-24
Structure title title	EVIDENCE FOR THE EXTENDED HELICAL NATURE OF POLYSACCHARIDE EPITOPES. THE 2.8 ANGSTROMS RESOLUTION STRUCTURE AND THERMODYNAMICS OF LIGAND BINDING OF AN ANTIGEN BINDING FRAGMENT SPECIFIC FOR ALPHA-(2->8)-POLYSIALIC ACID
Keywords keywords	IMMUNOGLOBULIN; IMMUNOGLOBULIN
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	25.44 Å
Radius of gyration Rg (electron density) rg_electron	24.37 Å
Forward intensity I(0) i0	37194900.00
Molecular weight molecular_weight	46719.0 kDa
Excluded volume excluded_volume	58190 Å³
Envelope volume envelope_volume	71809 Å³
Hydration-shell volume shell_volume	24750 Å³
Envelope diameter envelope_diameter	78.6 Å
Shell Rg shell_rg	31.47 Å
Envelope Rg envelope_rg	23.95 Å
Shape Rg shape_rg	24.35 Å
Total Rg total_rg	25.22 Å
Total atoms total_atoms	3291
Residues n_residues	430
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	76.9 Å
Rg (real space) rg_real	25.39 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	3.7190e+07
I(0) uncertainty (real space) i0_real_error	5.5190e+05
Rg (reciprocal space) rg_reciprocal	25.41 Å
I(0) (reciprocal space) i0_reciprocal	37200000.0000
Solution quality estimate total_estimate	0.9127
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.8 Å
Skewness Skewness skewness	0.225
Kurtosis Kurtosis kurtosis	-0.589
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6635000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.983; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.915

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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	IGG2A=KAPPA=
Molecular weight formula_weight	23737.3 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	3325

DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLYWYLQKPGQSPKPLIYRVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCFQGTHVPYTFGGGTRLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFN

Entity 2 Entity 2 polymer

Description description	IGG2A=KAPPA=
Molecular weight formula_weight	23022.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QIQLQQSGPELVRPGASVKISCKASGYTFTDYYIHWVKQRPGEGLEWIGWIYPGSGNTKYNEKFKGKATLTVDTSSSTAYMQLSSLTSEDSAVYFCARGGKFAMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIE

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1plgh1
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	d1plgh2
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	d1plgl1
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	d1plgl2
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	1plgH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1plgH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1plgL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1plgL02
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	79.140 Å
Unit-cell length b length_b	91.210 Å
Unit-cell length c length_c	141.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1640
R_work r_work	0.1640
R_free r_free	—

fit	/app/data/saxs_computation/pl/1plg/1plg.fit
pddf	/app/data/pr_computation/pl/1plg/1plg.pr.out
profile	/app/data/saxs_computation/pl/1plg/1plg.dat

EVIDENCE FOR THE EXTENDED HELICAL NATURE OF POLYSACCHARIDE EPITOPES. THE 2.8 ANGSTROMS RESOLUTION STRUCTURE AND THERMODYNAMICS OF LIGAND BINDING OF AN ANTIGEN BINDING FRAGMENT SPECIFIC FOR ALPHA-(2->8)-POLYSIALIC ACID

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

IGG2A=KAPPA=

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)