3w2d

Crystal Structure of Staphylococcal Eenterotoxin B in complex with a novel neutralization monoclonal antibody Fab fragment

Method: X-RAY DIFFRACTION D_max: 120.2 Å Quality: GOOD

▼

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

Enterotoxin type B

Staphylococcus aureus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 28–266	Not recorded	Monoclonal Antibody 3E2 Fab figment light chain × 1 Monoclonal Antibody 3E2 Fab figment heavy chain × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.10 Å R-free 0.261

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 3W2D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D5M X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH PEPTIDE AND SEB Deposited 1999-10-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 28–266（239 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；5% PEG 4000, 0.01 M NA ACETATE, PH 5, 2.4% ETHYLENE GLYCOL, pH 7.4	Resolution 2.00 Å R-free 0.260
1D5X X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH DIPEPTIDE MIMETIC AND SEB Deposited 1999-10-12	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.45 Å R-free 0.268
1D5Z X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH PEPTIDOMIMETIC AND SEB Deposited 1999-10-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.00 Å R-free 0.265
1D6E CRYSTAL STRUCTURE OF HLA-DR4 COMPLEX WITH PEPTIDOMIMETIC AND SEB Deposited 1999-10-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；pH 5	Resolution 2.45 Å R-free 0.226
1GOZ Structural basis for the altered T-cell receptor binding specificty in a superantigenic staphylococcus aureus Enterotoxin-B mutant Deposited 2001-10-29	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–266（239 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PH 4.6 SODIUM CITRATE BUFFER, 0.1M AMMONIUM ACETATE	Resolution 2.00 Å R-free 0.246
1GOZ Structural basis for the altered T-cell receptor binding specificty in a superantigenic staphylococcus aureus Enterotoxin-B mutant Deposited 2001-10-29	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–266（239 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；PH 4.6 SODIUM CITRATE BUFFER, 0.1M AMMONIUM ACETATE	Resolution 2.00 Å R-free 0.246
1SBB T-CELL RECEPTOR BETA CHAIN COMPLEXED WITH SUPERANTIGEN SEB Deposited 1999-02-22	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 28–266（239 aa） Chain D 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；CRYSTALLIZATION CONDITIONS: 10% PEG 8000 0.1M TRIS-HCL, PH8.5	Resolution 2.40 Å R-free 0.309
1SE3 STAPHYLOCOCCAL ENTEROTOXIN B COMPLEXED WITH GM3 TRISACCHARIDE Deposited 1996-10-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.8；24% PEG 4000, 20 MM BORATE BUFFER AT PH 8.8.	Resolution 2.30 Å R-free 0.330
1SE4 STAPHYLOCOCCAL ENTEROTOXIN B COMPLEXED WITH LACTOSE Deposited 1997-04-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.8；CRYSTALLIZED FROM 24% PEG 4000, 20 MM BORATE BUFFER AT PH 8.8 IN THE PRESENCE OF 100MM LACTOSE	Resolution 1.90 Å
1SEB COMPLEX OF THE HUMAN MHC CLASS II GLYCOPROTEIN HLA-DR1 AND THE BACTERIAL SUPERANTIGEN SEB Deposited 1995-11-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain D 29–262（234 aa） Chain H 29–262（234 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å R-free 0.327
2SEB X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH A PEPTIDE FROM HUMAN COLLAGEN II Deposited 1997-10-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 28–266（239 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1 M NA ACETATE PH 4.6 9 - 14% PEG 4000 0.2 M AMMONIUM ACETATE	Resolution 2.50 Å R-free 0.280
3GP7 Staphylococcal Enterotoxin B mutant N23YK97SK98S Deposited 2009-03-23	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–266（239 aa）	Mutation：N23Y, K97S, K98S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；18% (w/v) PEG 3350, 0.02% Na azide, pH8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.224
3GP7 Staphylococcal Enterotoxin B mutant N23YK97SK98S Deposited 2009-03-23	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–266（239 aa）	Mutation：N23Y, K97S, K98S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；18% (w/v) PEG 3350, 0.02% Na azide, pH8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.224
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	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 28–266（239 aa）	Not recorded	CL CHLORIDE ION × 3 SO4 SULFATE ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	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 28–266（239 aa）	Not recorded	CL CHLORIDE ION × 3 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 28–266（239 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 28–266（239 aa）	Not recorded	CL CHLORIDE ION × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 28–266（239 aa）	Not recorded	CL CHLORIDE ION × 3 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 28–266（239 aa）	Not recorded	CL CHLORIDE ION × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 28–266（239 aa）	Not recorded	CL CHLORIDE ION × 2 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3R8B Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8 Deposited 2011-03-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 28–266（239 aa）	Not recorded	CL CHLORIDE ION × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.265
3SEB STAPHYLOCOCCAL ENTEROTOXIN B Deposited 1997-11-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–265（238 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 1.48 Å
4RGM Structure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 20B1 Deposited 2014-09-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain S 28–266（239 aa） Fragment：UNP residues 28-266	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES sodium, pH 7.5, 20% w/v PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.69 Å R-free 0.277
4RGM Structure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 20B1 Deposited 2014-09-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 28–266（239 aa） Fragment：UNP residues 28-266	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES sodium, pH 7.5, 20% w/v PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.69 Å R-free 0.277
4RGN Structure of Staphylococcal Enterotoxin B bound to two neutralizing antibodies, 14G8 and 6D3 Deposited 2014-09-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 28–266（239 aa） Fragment：UNP residues 28-266	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；298 K；0.1 M phosphate/citrate, pH 4.2, 6.7% w/v PEG3000, 0.5 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.70 Å R-free 0.278
4RGN Structure of Staphylococcal Enterotoxin B bound to two neutralizing antibodies, 14G8 and 6D3 Deposited 2014-09-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain S 28–266（239 aa） Fragment：UNP residues 28-266	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；298 K；0.1 M phosphate/citrate, pH 4.2, 6.7% w/v PEG3000, 0.5 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.70 Å R-free 0.278
4RGO Structure of Staphylococcal Enterotoxin B bound to the neutralizing antibody 14G8 Deposited 2014-09-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain S 28–266（239 aa） Fragment：UNP residues 28-266	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；80 mM sodium cacodylate, pH 6.5, 16% w/v PEG8000, 160 mM magnesium acetate, 20% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.80 Å R-free 0.189
8YBL Crystal structure of nanobody SEB-Nb3 bound to staphylococcal enterotoxin B (SEB) Deposited 2024-02-15	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 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；8% v/v Tacsimate pH 5.0, 20% w/v Polyethylene glycol 3,350	Resolution 2.33 Å R-free 0.262
8YBM Crystal structure of nanobody SEB-Nb6 bound to staphylococcal enterotoxin B (SEB) Deposited 2024-02-15	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 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；2% v/v 1,4-Dioxane, 0.1 M Tris pH 8.0, 15% w/v Polyethylene glycol 3,350	Resolution 2.04 Å R-free 0.259
8YBM Crystal structure of nanobody SEB-Nb6 bound to staphylococcal enterotoxin B (SEB) Deposited 2024-02-15	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 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；2% v/v 1,4-Dioxane, 0.1 M Tris pH 8.0, 15% w/v Polyethylene glycol 3,350	Resolution 2.04 Å R-free 0.259
8YBN Crystal structure of nanobody SEB-Nb8 bound to staphylococcal enterotoxin B (SEB) Deposited 2024-02-15	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 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 20% w/v Polyethylene glycol 8,000	Resolution 2.18 Å R-free 0.281
8YBO Crystal structure of nanobody SEB-Nb11 bound to staphylococcal enterotoxin B (SEB) Deposited 2024-02-15	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 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；2% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.5, 20% w/v Polyethylene glycol 3,350	Resolution 1.59 Å R-free 0.284
8YBO Crystal structure of nanobody SEB-Nb11 bound to staphylococcal enterotoxin B (SEB) Deposited 2024-02-15	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 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；2% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.5, 20% w/v Polyethylene glycol 3,350	Resolution 1.59 Å R-free 0.284
8YBP Crystal structure of nanobody SEB-Nb20 bound to staphylococcal enterotoxin B (SEB) Deposited 2024-02-15	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 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2 M Magnesium sulfate heptahydrate, 20% w/v Polyethylene glycol 3,350	Resolution 2.08 Å R-free 0.253
8YKT Fab and SEB complex Deposited 2024-03-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 28–266（239 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Lithum sulfate, 0.1M Sodium acetate pH5.5, 10%PEG1000, 10% PEG8000	Resolution 2.04 Å R-free 0.230

22 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ETXB_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–239； UniProt 28–266

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3w2d
Deposition date deposition_date	2012-11-28
Structure title title	Crystal Structure of Staphylococcal Eenterotoxin B in complex with a novel neutralization monoclonal antibody Fab fragment
Keywords keywords	Staphylococcal Eenterotoxin B, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	34.10 Å
Radius of gyration Rg (electron density) rg_electron	34.20 Å
Forward intensity I(0) i0	89068400.00
Molecular weight molecular_weight	74677.0 kDa
Excluded volume excluded_volume	93081 Å³
Envelope volume envelope_volume	121230 Å³
Hydration-shell volume shell_volume	32606 Å³
Envelope diameter envelope_diameter	119.2 Å
Shell Rg shell_rg	37.09 Å
Envelope Rg envelope_rg	34.16 Å
Shape Rg shape_rg	34.14 Å
Total Rg total_rg	34.59 Å
Total atoms total_atoms	5258
Residues n_residues	663
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	120.2 Å
Rg (real space) rg_real	34.48 Å
Rg uncertainty (real space) rg_real_error	1.44 Å
I(0) (real space) i0_real	8.9070e+07
I(0) uncertainty (real space) i0_real_error	1.5080e+06
Rg (reciprocal space) rg_reciprocal	34.24 Å
I(0) (reciprocal space) i0_reciprocal	89050000.0000
Solution quality estimate total_estimate	0.8029
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	31.4 Å
Skewness Skewness skewness	0.611
Kurtosis Kurtosis kurtosis	-0.290
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11130000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.647; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.680; Smooth: 0.813

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Enterotoxin type B
Molecular weight formula_weight	28411.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5393

ESQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLGNYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCMYGGVTEHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNSPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKKK

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Monoclonal Antibody 3E2 Fab figment light chain
Molecular weight formula_weight	23460.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

ENVLTQSPAIMSASPGETVTMTCRATSSVSSTYLHWYQQKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQYINYPLTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Monoclonal Antibody 3E2 Fab figment heavy chain
Molecular weight formula_weight	24443.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

DVQLQESGPGLVRPSQSLSLTCTVTGYSLTSDFAWNWIRQFPGNKLEWMGYINYSGYTNYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCAREAYYGRAYWFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	135

▼

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3w2da1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.2 — Superantigen toxins, N-terminal domain

Domain ID domain_id	d3w2da2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.6 — Superantigen toxins, C-terminal domain
Family Family family	d.15.6.1 — Superantigen toxins, C-terminal domain

Domain ID domain_id	d3w2dh_
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	d3w2dl1
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.1.1.0 — automated matches

Domain ID domain_id	d3w2dl2
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 (6 domains)

Domain ID domain_id	3w2dA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	3w2dA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	3w2dH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3w2dH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3w2dL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3w2dL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	40.561 Å
Unit-cell length b length_b	109.308 Å
Unit-cell length c length_c	86.222 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.08 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	36.436 Å
R factor r_factor	0.1997
R_work r_work	0.1963
R_free r_free	0.2611

fit	/app/data/saxs_computation/w2/3w2d/3w2d.fit
pddf	/app/data/pr_computation/w2/3w2d/3w2d.pr.out
profile	/app/data/saxs_computation/w2/3w2d/3w2d.dat

Crystal Structure of Staphylococcal Eenterotoxin B in complex with a novel neutralization monoclonal antibody Fab fragment

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

Enterotoxin type B

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (5 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)