5vmr

Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.2110.4

Method: X-RAY DIFFRACTION D_max: 135.4 Å Quality: GOOD

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

Botulinum neurotoxin type B

Clostridium botulinum

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 A； UniProt 859–1291	Not recorded	Bot.2110.4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Magnesium acetate, 0.1 M Sodium acetate pH 5.0, 10 % PEG8000	Resolution 1.95 Å R-free 0.206
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 859–1291	Not recorded	Bot.2110.4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Magnesium acetate, 0.1 M Sodium acetate pH 5.0, 10 % PEG8000	Resolution 1.95 Å R-free 0.206

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 5VMR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EPW CRYSTAL STRUCTURE OF CLOSTRIDIUM NEUROTOXIN TYPE B Deposited 2000-03-29	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；PEG 4000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.90 Å R-free 0.233
1F31 CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH A TRISACCHARIDE Deposited 2000-05-31	Different construct 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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；PEG 4000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K	Resolution 2.60 Å R-free 0.270
1F82 BOTULINUM NEUROTOXIN TYPE B CATALYTIC DOMAIN Deposited 2000-06-28	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 1–424（424 aa） Fragment：CATALYTIC DOMAIN	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；294 K；Hepes, Polyethylene glycol MW 4000, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.20 Å R-free 0.276
1G9A CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH AN INHIBITOR (EXPERIMENT 3) Deposited 2000-11-22	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 2 BAB BIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；PEG 6000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K	Resolution 2.10 Å R-free 0.248
1G9B CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH AN INHIBITOR (EXPERIMENT 1) Deposited 2000-11-22	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 2 BAB BIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；PEG 6000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K	Resolution 2.00 Å R-free 0.243
1G9C CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH AN INHIBITOR (EXPERIMENT 4) Deposited 2000-11-22	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 2 BAB BIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；PEG 6000. MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K	Resolution 2.35 Å R-free 0.247
1G9D CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH AN INHIBITOR (EXPERIMENT 2) Deposited 2000-11-22	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 2 BAB BIS(5-AMIDINO-BENZIMIDAZOLYL)METHANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；PEG 6000. MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K	Resolution 2.20 Å R-free 0.283
1I1E CRYSTAL STRUCTURE OF CLOSTRIDIUM BOTULINUM NEUROTOXIN B COMPLEXED WITH DOXORUBICIN Deposited 2001-02-01	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 1–1290（1290 aa）	Not recorded	DM2 DOXORUBICIN × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；PEG 4000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K	Resolution 2.50 Å R-free 0.276
1S0B Crystal structure of botulinum neurotoxin type B at pH 4.0 Deposited 2003-12-30	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 1–1290（1290 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；298 K；PEG 4000, MES, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.00 Å R-free 0.235
1S0C Crystal structure of botulinum neurotoxin type B at pH 5.0 Deposited 2003-12-30	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；PEG 4000, MES, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.20 Å R-free 0.240
1S0D Crystal structure of botulinum neurotoxin type B at pH 5.5 Deposited 2003-12-30	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；PEG 4000, MES, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.20 Å R-free 0.273
1S0E Crystal structure of botulinum neurotoxin type B at pH 6.0 Deposited 2003-12-30	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；298 K；PEG 4000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 6.00	Resolution 1.90 Å R-free 0.232
1S0F Crystal structure of botulinum neurotoxin type B at pH 7.0 Deposited 2003-12-30	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 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；298 K；PEG 4000, MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00	Resolution 2.30 Å R-free 0.288
1S0G Crystal structure of botulinum neurotoxin type B apo form Deposited 2003-12-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1290（1290 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；PEG 4000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.265
1Z0H N-terminal helix reorients in recombinant C-fragment of Clostridium botulinum type B Deposited 2005-03-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 853–1290（438 aa） Fragment：sequence database residues 853-1290	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Ammonium Formate, PEG6000, Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.282
1Z0H N-terminal helix reorients in recombinant C-fragment of Clostridium botulinum type B Deposited 2005-03-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 853–1290（438 aa） Fragment：sequence database residues 853-1290	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Ammonium Formate, PEG6000, Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.282
2ETF Crystal structure of full length botulinum neurotoxin (Type B) light chain Deposited 2005-10-27	Different construct 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 0–440（441 aa） Fragment：Catalytic Domain (residues 0-440)	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；Ammonium sulphate, Sodium Cacodylate, pH 6.2, VAPOR DIFFUSION, SITTING DROP	Resolution 2.29 Å R-free 0.264
2ETF Crystal structure of full length botulinum neurotoxin (Type B) light chain Deposited 2005-10-27	Different construct 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 0–440（441 aa） Fragment：Catalytic Domain (residues 0-440)	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；Ammonium sulphate, Sodium Cacodylate, pH 6.2, VAPOR DIFFUSION, SITTING DROP	Resolution 2.29 Å R-free 0.264
2NM1 Structure of BoNT/B in complex with its protein receptor Deposited 2006-10-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 857–1290（434 aa） Fragment：receptor binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；293 K；13% PEG 6000, 0.1M Hepes, pH 7.0, EVAPORATION, temperature 293K	Resolution 2.15 Å R-free 0.246
2NP0 Crystal structure of the Botulinum neurotoxin type B complexed with synaptotagamin-II ectodomain Deposited 2006-10-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；297 K；0.4 M (NH4)2SO4, 0.9 M Li2SO4, and 0.1 M sodium citrate at pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.62 Å R-free 0.227
2NP0 Crystal structure of the Botulinum neurotoxin type B complexed with synaptotagamin-II ectodomain Deposited 2006-10-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1290（1290 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 6 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；297 K；0.4 M (NH4)2SO4, 0.9 M Li2SO4, and 0.1 M sodium citrate at pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.62 Å R-free 0.227
2XHL Structure of a functional derivative of Clostridium botulinum neurotoxin type B Deposited 2010-06-18	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 1–437（437 aa） Fragment：RESIDUES 1-437 Chain B 446–858（413 aa） Fragment：RESIDUES 446-858	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；15% PEG3350, 0.1M BIS-TRIS-PROPANE PH 6.5, 0.2M SODIUM SULPHATE	Resolution 2.80 Å R-free 0.282
3ZUQ Crystal structure of an engineered botulinum neurotoxin type B - derivative, LC-B-GS-Hn-B Deposited 2011-07-19	Different construct 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 1–437（437 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-437, TRANSLOCATION DOMAIN, RESIDUES 446-858 Chain A 446–858（413 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 1-437, TRANSLOCATION DOMAIN, RESIDUES 446-858	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.1M TRIS ACETATE PH8.0, 0.2M MGCL, 20% PEG8000	Resolution 2.70 Å R-free 0.281
4KBB Structure of Botulinum neurotoxin B binding domain in complex with both synaptotagmin II and GD1a Deposited 2013-04-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 857–1291（435 aa） Fragment：UNP residues 857-1291	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；292 K；0.2 M MgCl2, 0.1 M Hepes pH 7.0 -7.2 and 20-24% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.30 Å R-free 0.189
4KBB Structure of Botulinum neurotoxin B binding domain in complex with both synaptotagmin II and GD1a Deposited 2013-04-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 857–1291（435 aa） Fragment：UNP residues 857-1291	Not recorded	CL CHLORIDE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；292 K；0.2 M MgCl2, 0.1 M Hepes pH 7.0 -7.2 and 20-24% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.30 Å R-free 0.189
5VID Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.0671.2 Deposited 2017-04-15	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM Tris, pH 8.0, 25 % PEG 400	Resolution 2.75 Å R-free 0.232
5VID Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.0671.2 Deposited 2017-04-15	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM Tris, pH 8.0, 25 % PEG 400	Resolution 2.75 Å R-free 0.232
5VID Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.0671.2 Deposited 2017-04-15	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM Tris, pH 8.0, 25 % PEG 400	Resolution 2.75 Å R-free 0.232
5VID Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.0671.2 Deposited 2017-04-15	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM Tris, pH 8.0, 25 % PEG 400	Resolution 2.75 Å R-free 0.232
5VID Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.0671.2 Deposited 2017-04-15	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM Tris, pH 8.0, 25 % PEG 400	Resolution 2.75 Å R-free 0.232
6G5F Crystal structure of an engineered Botulinum Neurotoxin type B mutant E1191M/S1199Y in complex with human synaptotagmin 1 Deposited 2018-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1291（1291 aa） Chain B 1–1291（1291 aa）	Mutation：E231Q, H234Y Mutation：E231Q, H234Y	GOL GLYCEROL × 3 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；1.1 M sodium malonate dibasic monohydrate, HEPES pH 7.0, 0.5% v/v Jeffamine ED-2003	Resolution 2.50 Å R-free 0.232
6G5G Crystal structure of an engineered Botulinum Neurotoxin type B mutant E1191M/S1199Y in complex with human synaptotagmin 2 Deposited 2018-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1291（1291 aa） Chain B 1–1291（1291 aa）	Mutation：E231Q, H234Y Mutation：E231Q, H234Y	MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 ACT ACETATE ION × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；0.2 M magnesium chloride, Tris pH 7.0, 10% w/v PEG 8000	Resolution 2.00 Å R-free 0.223
6G5K Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with human synaptotagmin 1 Deposited 2018-03-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 857–1291（435 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.1 M Amino acids 0.1 M Buffer System 2 7.5 50 % v/v Precipitant Mix 1	Resolution 2.00 Å R-free 0.235
6G5K Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with human synaptotagmin 1 Deposited 2018-03-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 857–1291（435 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.1 M Amino acids 0.1 M Buffer System 2 7.5 50 % v/v Precipitant Mix 1	Resolution 2.00 Å R-free 0.235
6QNS Crystal structure of the binding domain of Botulinum Neurotoxin type B mutant I1248W/V1249W in complex with human synaptotagmin 1 and GD1a receptors Deposited 2019-02-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 857–1291（435 aa）	Mutation：I1248W, V1249W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294.15 K；20% v/v PEG6000, 0.1 M MES pH 6.0, 0.2 M sodium chloride	Resolution 2.40 Å R-free 0.229
6UC6 Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-H11 Deposited 2019-09-15	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M KCl, 15 % PEG 5000 MME, 0.1 M MES	Resolution 2.32 Å R-free 0.222
6UC6 Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-H11 Deposited 2019-09-15	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M KCl, 15 % PEG 5000 MME, 0.1 M MES	Resolution 2.32 Å R-free 0.222
6UFT Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLK-G12 Deposited 2019-09-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 859–1291（433 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M ammonium sulfate, 14 % PEG 8000, 0.1 M MES pH 6.0	Resolution 2.90 Å R-free 0.258
6UHT Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-G10 Deposited 2019-09-28	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；15 % PEG 20000 and 0.1 M MES pH 6.5	Resolution 2.20 Å R-free 0.211
6UHT Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-G10 Deposited 2019-09-28	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 859–1291（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；15 % PEG 20000 and 0.1 M MES pH 6.5	Resolution 2.20 Å R-free 0.211
6UL4 Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLO-G11 Deposited 2019-10-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 859–1291（433 aa） Fragment：receptor-binding domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；20 % Ethanol, 0.1 M Tris	Resolution 3.18 Å R-free 0.258
7NA9 Crystal structure of BoNT/B-LC-JSG-C1 Deposited 2021-06-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–441（441 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG4000	Resolution 1.76 Å R-free 0.205
7QFQ Cryo-EM structure of Botulinum neurotoxin serotype B Deposited 2021-12-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1291（1291 aa）	Mutation：E231Q, H234Y	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES pH7.5, 50mM NaCl, 0.5mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7T5F Botulinum neurotoxin Type B Light Chain complexed with nanobodies JLJ-G3 and JNE-B10 Deposited 2021-12-12	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 A 1–425（425 aa）	Not recorded	ZN ZINC ION × 1 IOD IODIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M KI, 0.1 M MES pH 6.5, 25 % PEG 4000	Resolution 2.60 Å R-free 0.222
7T5F Botulinum neurotoxin Type B Light Chain complexed with nanobodies JLJ-G3 and JNE-B10 Deposited 2021-12-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–425（425 aa）	Not recorded	ZN ZINC ION × 1 IOD IODIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M KI, 0.1 M MES pH 6.5, 25 % PEG 4000	Resolution 2.60 Å R-free 0.222

33 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BXB_CLOBO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–438； UniProt 859–1291 Author chain B； PDBConstruct 6–438； UniProt 859–1291

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	5vmr
Deposition date deposition_date	2017-04-28
Structure title title	Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.2110.4
Keywords keywords	mini-protein binder, inhibitor, TOXIN; TOXIN
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	41.35 Å
Radius of gyration Rg (electron density) rg_electron	41.25 Å
Forward intensity I(0) i0	164515000.00
Molecular weight molecular_weight	108620.0 kDa
Excluded volume excluded_volume	137310 Å³
Envelope volume envelope_volume	184340 Å³
Hydration-shell volume shell_volume	38124 Å³
Envelope diameter envelope_diameter	141.6 Å
Shell Rg shell_rg	45.59 Å
Envelope Rg envelope_rg	40.49 Å
Shape Rg shape_rg	41.23 Å
Total Rg total_rg	41.55 Å
Total atoms total_atoms	7691
Residues n_residues	915
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	135.4 Å
Rg (real space) rg_real	41.56 Å
Rg uncertainty (real space) rg_real_error	1.28 Å
I(0) (real space) i0_real	1.6450e+08
I(0) uncertainty (real space) i0_real_error	3.0830e+06
Rg (reciprocal space) rg_reciprocal	41.35 Å
I(0) (reciprocal space) i0_reciprocal	164500000.0000
Solution quality estimate total_estimate	0.8207
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	28.5 Å
Skewness Skewness skewness	0.324
Kurtosis Kurtosis kurtosis	-0.771
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30370000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.764; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.776; Smooth: 0.596

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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	Botulinum neurotoxin type B
Molecular weight formula_weight	52534.1 kDa
EC 编号 ec_number	3.4.24.69
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8308

GPLGSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSSANSKIRVTQNQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSGWKISIRGNRIIWTLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLNNAKIYINGKLESNTDIKDIREVIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKIQSYSEYLKDFWGNPLMYNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKSNSQSINDDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDSDEFYNTIQIKEYDEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEEYKDYFCISKWYLKEVKRKPYNLKLGCNWQFIPKDEGWTE

来源 Source

来源生物 organism	Clostridium botulinum
NCBI Class编号 ncbi_taxonomy_id	1491
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Bot.2110.4
Molecular weight formula_weight	4928.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

PDMFCALKIKFFLEIGDEDAARKAAKKCGYSEEQAERIIKKNL

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	575

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5vmrA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	5vmrA02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	5vmrB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	5vmrB02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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8. Citations (1)

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Unit-cell length a length_a	38.698 Å
Unit-cell length b length_b	246.477 Å
Unit-cell length c length_c	64.364 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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	19.969 Å
R factor r_factor	0.1827
R_work r_work	0.1814
R_free r_free	0.2059

fit	/app/data/saxs_computation/vm/5vmr/5vmr.fit
pddf	/app/data/pr_computation/vm/5vmr/5vmr.pr.out
profile	/app/data/saxs_computation/vm/5vmr/5vmr.dat

Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.2110.4

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

Botulinum neurotoxin 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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)