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Department of Biochemistry and Molecular Biology Sealy Center for Structural Biology Computational Biology



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                SDAP - Structural Database of Allergenic Proteins
Go to: SDAP All allergens       Go to: SDAP Food allergens
Send a comment to Werner Braun      Submit new allergen information to SDAP
  
Alphabetical listing of allergens: A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
Access to SDAP is available free of charge for Academic and non-profit use.
Licenses for commercial use can be obtained by contacting W. Braun (webraun@utmb.edu).
Secure access to SDAP is available from https://fermi.utmb.edu/SDAP
Allergen Info Description
Allergen ID 202
Allergen Scientific Name Api m 1
Allergen Species - Systematic Name Apis mellifera
Allergen Species - Common Name honey bee
Allergen Common source insects
Allergen Common name
Allergen Keywords phospholipase A2; Phosphatidylcholine 2-acylhydrolase; EC 3.1.1.4
Allergen IUIS (Yes=1, No=0) 1
ID Allergen Name
Api m 1 - References
ID Reference
Pubmed ID: 2444130
Weber A, Schroder H, Thalberg K, Marz L, Specific interaction of IgE antibodies with a carbohydrate epitope of honey bee venom phospholipase A2. Allergy. 1987 Aug;42(6):464-70.
Pubmed ID: 9751842
Blaser K, Carballido J, Faith A, Crameri R, Akdis C, Determinants and mechanisms of human immune responses to bee venom phospholipase A2. Int Arch Allergy Immunol. 1998 Sep;117(1):1-10.
Pubmed ID: 9648701
Muller U, Akdis CA, Fricker M, Akdis M, Blesken T, Bettens F, Blaser K, Successful immunotherapy with T-cell epitope peptides of bee venom phospholipase A2 induces specific T-cell anergy in patients allergic to bee venom. J Allergy Clin Immunol. 1998 Jun;101(6 Pt 1):747-54.
Pubmed ID: 7682244
Carballido JM, Carballido-Perrig N, Kagi MK, Meloen RH, Wuthrich B, Heusser CH, Blaser K, T cell epitope specificity in human allergic and nonallergic subjects to bee venom phospholipase A2. J Immunol. 1993 Apr 15;150(8 Pt 1):3582-91.
Pubmed ID: 2776767
Kuchler K, Gmachl M, Sippl MJ, Kreil G, Analysis of the cDNA for phospholipase A2 from honeybee venom glands. The deduced amino acid sequence reveals homology to the corresponding vertebrate enzymes. Eur J Biochem. 1989 Sep 1;184(1):249-54.
Pubmed ID: 15459335
Buhot C, Chenal A, Sanson A, Pouvelle-Moratille S, Gelb MH, Menez A, Gillet Alteration of the tertiary structure of the major bee venom allergen Api m 1 by multiple mutations is concomitant with low IgE reactivity. Protein Sci. 2004 Nov;13(11):2970-8. Epub 2004 Sep 30.
Api m 1 - Protein Sequences
Source Link to source
SwissProt P00630
Api m 1 - PDB Structure
PDB Id PDB Name PDB Entry Deposition Date Experiment Type Observation
202 150 1POC 07-SEP-92 X-ray diffraction resolution 2.0 A complex with transition-state analogue
1POC.pdb


Api m 1 - Sequence Search
Sequence Header Sequence
Api m 1
SDAP Sequence ID: 31
SDAP Allergen ID: 202
GSLFLLLLSTSHGWQIRDRIGDNELEERIIYPGTLWCGHGNKSSGPNELGRFKHTDACCRTHDMCPDVMSAGESKHGLTNTASHTRLSCDCDDKFYDCLKNSADTISSYFVGKMYFNLIDTKCYKLEHPVTGCGERTEGRCLHYTVDKSKPKVYQWFDLRKY
View 3D Structure Click here to view 3D model structure of allergen
Fasta Search in SDAP
Blast Swissprot database search at NCBI
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Expasy Blast Search
Api m 1 - Statistics from Alphafold ( SI is sequence id, Best template format: PDB_ChainID)
Allergen Name pLDDT Score pTM Score Best PDB template %Seq ID Align length Seq length Query Range Sequence Range E-Value Bit Score Download Model
Api m 1 87.75 0.74 1POC_A 100 134 162 29 - 162 1 - 134 0 282 Download (SI: 31)
Api m 1 - Alphafold Theoretical Model Structure
Model Structure
31_relaxed_rank_1_model_2.pdb


Coverage Plddt
Api m 1 - Protein Sequence Properties!
Protein Sequence Protease cleavage sites PeptideCutter at ExPASy
P00630 Click here to process the data
Api m 1 - PFAM Information
SeqID Aller ID AlnS AlnE EnvS EnvE PFAM ID Family Type Clan Description
31 202 30 126 30 127 PF05826 Phospholip_A2_2 Domain CL0629 Phospholipase A2
Where: AlnS= Alignment start position, AlnE= Alignment end position, EnvS= Envelope start position, EnvE= Envelope end position.

Welcome

Predicted B-Cell epitope using BCEP method for Api m 1

Probe radius : 1.400

POLAR area/energy = 3944.89

APOLAR area/energy = 7260.31

Total area/energy = 11205.20

Number of surface atoms = 855

Number of buried atoms = 439

Residues Predicted with high probability (in top five patches) are: 30,31,32,33,12,13,14,15,16,11,96,100,109,113,115,117,160,161,162,18,46 , and medium probability (next top five patches) are : 46,63,64,65,66,28,36,38,39,40,41,42,85,89,122,125,127,144,155,156,157,158 . Predicted residues are shown in red and green color stick representation.

Original PDB file 4893.test.pdb
Original PDB file with surface residue only. All amino acid residue are replaced by their CB atom, in case of GLY CA atom is used. Solvent accessible surface area of each residue is stored in last column of the PDB file. 14893.test.txt
Patch drawn around the residues by patch analysis are stored in this file
How to read: Col 1: Patch No. Col 2: Center Res Name. Col 3: Sum(Pint*Area), Col 4: Sum(Psur*Area), Col 5: Total Residue, Col 6: Interface score, Col 7: Surface Score, Col 8: Max Interface Score, Col 9: Minimum Interface Score
4893.test.tmppat
Residues predicted by patch analysis are stored in this file.
How to read: Col 1: Patch No. Col 2: Center Res Name. Col 3: Res Number Col 4: Neigbouring Res Name, Col 5: Sum(Pint*Area). Col 6: Sum(PSur*Area), Col 7: Sum(Area), Col 8: Similar no of residue in patch (e.g CYS, CYS = 2)
4893.test.res
All residues scored by patch analysis are stored in this file.
How to read: Col 1: Patch No. Col 2: Center Res Name. Col 3: Sum(Pint*Area)/sum(Area), Col 4: Sum(Psur*Area)/sum(Area), Col 5: Total Residue
4893.test.resALL

[For BCEP predicted results, please cite our websites http://fermi.utmb.edu/ http://curie.utmb.edu/ for your future publications (Negi et al., Bioinformatics, 23, 3397-3399, 2007 , Negi et al., J. Mol. Model., 13, 1157-1167, 2007; Negi et al., J. Mol. Model., 12, 921-929, 2006)]



List of B-cell epitopes predicted by BepiPred method using a window size of 9 amino acids
Peptides predicted from BepiPred method can be used to search related peptides in SDAP using PD search and Cross-React method.
Please note: BepiPred Epitopes are predicted using BepiPred webserver implemented in IEDB Analysis Resource at http://tools.iedb.org/main/bcell/
Cleck here for epitopes predicted by BepiPred method

Api m 1 - Epitope Information from published data
No. Position Epitope Sequence Epitope Type View epitope Search epitope in SDAP PD search in SDAP Cross-React search
No epitope information found!
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