4bkc

Crystal Structure of a unusually linked dimeric variant of Bet v 1

Method: X-RAY DIFFRACTION D_max: 76.3 Å Quality: GOOD

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

MAJOR POLLEN ALLERGEN BET V 1-A

BETULA PENDULA

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–160 Chain B； UniProt 2–160	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；0.1 M NA ACETATE PH 6.5, 27 % PEG 3350	Resolution 1.73 Å R-free 0.247

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 4BKC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B6F BIRCH POLLEN ALLERGEN BET V 1 Deposited 1999-01-13	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 1–159（159 aa）	Mutation：M139L	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1	Resolution not provided
1BTV STRUCTURE OF BET V 1, NMR, 20 STRUCTURES Deposited 1997-01-30	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 2–160（159 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1BV1 BIRCH POLLEN ALLERGEN BET V 1 Deposited 1997-07-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–160（159 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.3；PROTEIN WAS CRYSTALLIZED BY MIXING 5 MG/ML PROTEIN SOLUTION WITH EQUAL AMOUNT OF 2.0 M AMS, 100 MM SODIUM CITRATE, PH 6.3	Resolution 2.00 Å R-free 0.267
1FSK COMPLEX FORMATION BETWEEN A FAB FRAGMENT OF A MONOCLONAL IGG ANTIBODY AND THE MAJOR ALLERGEN FROM BIRCH POLLEN BET V 1 Deposited 2000-09-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–159（159 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；300 K；12% peg 6000, 0.1M sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.90 Å R-free 0.285
1FSK COMPLEX FORMATION BETWEEN A FAB FRAGMENT OF A MONOCLONAL IGG ANTIBODY AND THE MAJOR ALLERGEN FROM BIRCH POLLEN BET V 1 Deposited 2000-09-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–159（159 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；300 K；12% peg 6000, 0.1M sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.90 Å R-free 0.285
1FSK COMPLEX FORMATION BETWEEN A FAB FRAGMENT OF A MONOCLONAL IGG ANTIBODY AND THE MAJOR ALLERGEN FROM BIRCH POLLEN BET V 1 Deposited 2000-09-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–159（159 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；300 K；12% peg 6000, 0.1M sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.90 Å R-free 0.285
1FSK COMPLEX FORMATION BETWEEN A FAB FRAGMENT OF A MONOCLONAL IGG ANTIBODY AND THE MAJOR ALLERGEN FROM BIRCH POLLEN BET V 1 Deposited 2000-09-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1–159（159 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；300 K；12% peg 6000, 0.1M sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.90 Å R-free 0.285
1LLT BIRCH POLLEN ALLERGEN BET V 1 MUTANT E45S Deposited 2002-04-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–160（159 aa）	Mutation：E45S	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.10 Å R-free 0.301
1QMR BIRCH POLLEN ALLERGEN BET V 1 MUTANT N28T, K32Q, E45S, P108G Deposited 1999-10-06	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–159（159 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.00	Resolution 2.15 Å R-free 0.238
4A80 Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in complex with 8-Anilinonaphthalene-1-sulfonate (ANS) Deposited 2011-11-18	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 2–160（159 aa）	Not recorded	2AN 8-ANILINO-1-NAPHTHALENE SULFONATE × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 1.96 Å R-free 0.205
4A81 Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in ternary complex with 8-Anilinonaphthalene-1-sulfonate (ANS) and deoxycholic acid Deposited 2011-11-18	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 2–160（159 aa）	Not recorded	SO4 SULFATE ION × 1 DXC (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID × 1 2AN 8-ANILINO-1-NAPHTHALENE SULFONATE × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 2.05 Å R-free 0.230
4A83 Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in complex with deoxycholate. Deposited 2011-11-18	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 2–160（159 aa）	Not recorded	DXC (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID × 2 SO4 SULFATE ION × 5 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 1.54 Å R-free 0.168
4A84 Crystal Structure of Major Birch Pollen Allergen Bet v 1 a F30V mutant in complex with deoxycholate. Deposited 2011-11-18	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 2–160（159 aa）	Mutation：YES	DXC (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 1.50 Å R-free 0.243
4A85 Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in complex with kinetin. Deposited 2011-11-18	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 2–160（159 aa）	Not recorded	H35 N-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE × 1 SO4 SULFATE ION × 5 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 1.40 Å R-free 0.180
4A86 Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in ternary complex with kinetin and 8-Anilinonaphthalene-1-sulfonate (ANS) Deposited 2011-11-18	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 2–160（159 aa）	Not recorded	2AN 8-ANILINO-1-NAPHTHALENE SULFONATE × 1 H35 N-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 1.59 Å R-free 0.207
4A87 Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in complex with naringenin. Deposited 2011-11-18	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 2–160（159 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 NAR NARINGENIN × 1 NA SODIUM ION × 1 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 1.24 Å R-free 0.162
4A88 Crystal Structure of native Major Birch Pollen Allergen Bet v 1 isoform a Deposited 2011-11-18	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 2–160（159 aa）	Not recorded	SO4 SULFATE ION × 7 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 1.51 Å R-free 0.168
4A8G Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in complex with dimethylbenzylammonium propane sulfonate Deposited 2011-11-21	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 2–160（159 aa）	Not recorded	DMX 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 2.10 Å R-free 0.249
4B9R Crystal structure of the Major Birch Pollen Allergen Bet v 1.0101 (isoform a) nitrated in vitro with tetranitromethan. Deposited 2012-09-06	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 2–160（159 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；2M AMMONIUM SULFATE 1.5% 2-METHYL-2,4-PENTANDIOL, pH 7	Resolution 1.76 Å R-free 0.249
4BK6 Crystal Structure of a dimeric variant of Bet v 1 Deposited 2013-04-22	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–160（159 aa） Chain B 2–160（159 aa）	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；27 % PEG 3350, 0.1 M NA-ACETAT TRIHYDRATE PH 5.5	Resolution 1.63 Å R-free 0.238
4BK7 Crystal Structure of a variant of the Major Birch Pollen Allergen Bet v 1 Deposited 2013-04-22	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 2–160（159 aa）	Mutation：YES	SO4 SULFATE ION × 5 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；2M AMMONIUM SULFATE, 1.5 % MPD, pH 4.5	Resolution 1.14 Å R-free 0.175
4BKD Crystal Structure of an unusually linked dimeric variant of Bet v 1 (b) Deposited 2013-04-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–160（159 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；27 % PEG 3350, 0.1 M NA-ACETATE, PH 6.5	Resolution 1.17 Å R-free 0.202
4BTZ Crystal Structure of peroxinitrite treated Major Birch Pollen Allergen Bet v 1.0101 (isoform a) Deposited 2013-06-19	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 2–160（159 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 1.47 Å R-free 0.235
4MNS Crystal structure of the major pollen allergen Bet v 1-A in complex with P303 Deposited 2013-09-11	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 2–160（159 aa） Fragment：UNP residues 2-160	Not recorded	2AX (3R,4R,5aR,11aR)-3-methyl-6,11-dioxo-2,3,4,5,5a,6,11,11a-octahydrothiepino[3,2-g]isoquinoline-4-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；28% PEG MME 2000, 20mM ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.20 Å R-free 0.160
4QIP Crystal Structure of Major Birch Pollen Allergen Bet v 1 isoform a in complex with Sodium Dodecyl Sulfate Deposited 2014-06-01	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 2–160（159 aa） Fragment：UNP residues 2-160	Mutation：D125A	SDS DODECYL SULFATE × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；2M AMMONIUM SULFATE 1.5% 2-METHYL-2,4-PENTANDIOL, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.288
4Z3L CRYSTAL STRUCTURE OF BIRCH POLLEN ALLERGEN BET V 1 MUTANT G26L, D69I, P90L, K97I Deposited 2015-03-31	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 2–160（159 aa）	Mutation：G26L D69I P90L K97I	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；25% PEG8000, 0.2 M lithium sulfate, 0.1 M HEPES pH 7.4	Resolution 2.50 Å R-free 0.256
4Z3L CRYSTAL STRUCTURE OF BIRCH POLLEN ALLERGEN BET V 1 MUTANT G26L, D69I, P90L, K97I Deposited 2015-03-31	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 2–160（159 aa）	Mutation：G26L D69I P90L K97I	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；25% PEG8000, 0.2 M lithium sulfate, 0.1 M HEPES pH 7.4	Resolution 2.50 Å R-free 0.256
4Z3L CRYSTAL STRUCTURE OF BIRCH POLLEN ALLERGEN BET V 1 MUTANT G26L, D69I, P90L, K97I Deposited 2015-03-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2–160（159 aa）	Mutation：G26L D69I P90L K97I	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；25% PEG8000, 0.2 M lithium sulfate, 0.1 M HEPES pH 7.4	Resolution 2.50 Å R-free 0.256
4Z3L CRYSTAL STRUCTURE OF BIRCH POLLEN ALLERGEN BET V 1 MUTANT G26L, D69I, P90L, K97I Deposited 2015-03-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 2–160（159 aa）	Mutation：G26L D69I P90L K97I	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；25% PEG8000, 0.2 M lithium sulfate, 0.1 M HEPES pH 7.4	Resolution 2.50 Å R-free 0.256
4Z3L CRYSTAL STRUCTURE OF BIRCH POLLEN ALLERGEN BET V 1 MUTANT G26L, D69I, P90L, K97I Deposited 2015-03-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 2–160（159 aa）	Mutation：G26L D69I P90L K97I	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；25% PEG8000, 0.2 M lithium sulfate, 0.1 M HEPES pH 7.4	Resolution 2.50 Å R-free 0.256
4Z3L CRYSTAL STRUCTURE OF BIRCH POLLEN ALLERGEN BET V 1 MUTANT G26L, D69I, P90L, K97I Deposited 2015-03-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 2–160（159 aa）	Mutation：G26L D69I P90L K97I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；25% PEG8000, 0.2 M lithium sulfate, 0.1 M HEPES pH 7.4	Resolution 2.50 Å R-free 0.256
6R3C Solution structure of birch pollen allergen Bet v 1a Deposited 2019-03-20	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 2–160（159 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.5 mM [U-13C; U-15N] Betv1a, 0.05 mM sodium chloride, 0.05 mM sodium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
7MXL Complex of Bet v 1 with the Fab fragments of a three antibody cocktail Deposited 2021-05-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain C 1–160（160 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7N0U Complex of recombinant Bet v 1 with Fab fragment of REGN5713 Deposited 2021-05-26	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 C 2–160（159 aa）	Mutation：F63L	SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；ammonium sulfate, sodium acetate, glycerol	Resolution 3.00 Å R-free 0.280
7N0V Complex of recombinant Bet v 1 with Fab fragment of REGN5715 Deposited 2021-05-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 2–160（159 aa）	Mutation：F63L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；PEG3350, PEG 400, Mg acetate	Resolution 3.71 Å R-free 0.378
9Y0A Crystal structure of Bet v 1.0101 in complex with human IgE Fab 2H22 Deposited 2025-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–160（160 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 3 PG4 TETRAETHYLENE GLYCOL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES pH 7.5; 0.05 M magnesium chloride hexahydrate; 30% PEG MME 550	Resolution 2.12 Å R-free 0.218
9Y0E Crystal structure of Bet v 1.0101 in complex with human IgE Fab 2H22 Deposited 2025-08-28	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 C 1–160（160 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.04 M potassium phosphate monobasic; 16% PEG 8000; 20% glycerol	Resolution 2.90 Å R-free 0.257

29 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BEV1A_BETPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–159； UniProt 2–160 Author chain B； PDBConstruct 1–159； UniProt 2–160

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	4bkc
Deposition date deposition_date	2013-04-23
Structure title title	Crystal Structure of a unusually linked dimeric variant of Bet v 1
Keywords keywords	ALLERGEN, DIMERISATION, POLYSULFIDE, SULFUR INCORPORATION; ALLERGEN
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	23.11 Å
Radius of gyration Rg (electron density) rg_electron	22.34 Å
Forward intensity I(0) i0	20756400.00
Molecular weight molecular_weight	34879.0 kDa
Excluded volume excluded_volume	43800 Å³
Envelope volume envelope_volume	53651 Å³
Hydration-shell volume shell_volume	20946 Å³
Envelope diameter envelope_diameter	79.6 Å
Shell Rg shell_rg	28.05 Å
Envelope Rg envelope_rg	22.17 Å
Shape Rg shape_rg	22.38 Å
Total Rg total_rg	23.00 Å
Total atoms total_atoms	2458
Residues n_residues	316
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	76.3 Å
Rg (real space) rg_real	23.16 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	2.0760e+07
I(0) uncertainty (real space) i0_real_error	3.0630e+05
Rg (reciprocal space) rg_reciprocal	23.15 Å
I(0) (reciprocal space) i0_reciprocal	20760000.0000
Solution quality estimate total_estimate	0.7994
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.7 Å
Skewness Skewness skewness	0.401
Kurtosis Kurtosis kurtosis	-0.380
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4262000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4bkca_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.3 — Bet v1-like
Family Family family	d.129.3.1 — Pathogenesis-related protein 10 (PR10)-like

Domain ID domain_id	d4bkcb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.3 — Bet v1-like
Family Family family	d.129.3.1 — Pathogenesis-related protein 10 (PR10)-like

CATH v4.4 (2 domains)

Domain ID domain_id	4bkcA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	530 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4
Homologous superfamily homologous superfamily	20 — START domain

Domain ID domain_id	4bkcB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	530 — Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4
Homologous superfamily homologous superfamily	20 — START domain

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8. Citations (1)

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Unit-cell length a length_a	39.880 Å
Unit-cell length b length_b	60.950 Å
Unit-cell length c length_c	59.720 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.47 °
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	1.730 Å
Low-resolution limit resolution_low	56.970 Å
R factor r_factor	0.2036
R_work r_work	0.2012
R_free r_free	0.2467

Description description	MAJOR POLLEN ALLERGEN BET V 1-A
Molecular weight formula_weight	17465.7 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2752

Crystal Structure of a unusually linked dimeric variant of Bet v 1

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

MAJOR POLLEN ALLERGEN BET V 1-A

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	BETULA PENDULA
通用名 common_name	EUROPEAN WHITE BIRCH
NCBI Class编号 ncbi_taxonomy_id	3505
宿主生物 host_organism	ESCHERICHIA COLI

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	219

fit	/app/data/saxs_computation/bk/4bkc/4bkc.fit
pddf	/app/data/pr_computation/bk/4bkc/4bkc.pr.out
profile	/app/data/saxs_computation/bk/4bkc/4bkc.dat