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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 9
Allergen Scientific Name Amb t 5
Allergen Species - Systematic Name Ambrosia trifida
Allergen Species - Common Name giant ragweed
Allergen Common source weed
Allergen Common name Asterales
Allergen Keywords Ra5G
Allergen IUIS (Yes=1, No=0) 1
ID Allergen Name
Amb t 5 - References
ID Reference
Pubmed ID: 1606135
Metzler WJ, Valentine K, Roebber M, Friedrichs MS, Marsh DG, Mueller L, Determination of the three-dimensional solution structure of ragweed allergen Amb t V by nuclear magnetic resonance spectroscopy. Biochemistry. 1992 Jun 9;31(22):5117-27.
Pubmed ID: 3856613
Roebber M, Klapper DG, Goodfriend L, Bias WB, Hsu SH, Marsh DG, Immunochemical and genetic studies of Amb.t. V (Ra5G), an Ra5 homologue from giant ragweed pollen. J Immunol. 1985 May;134(5):3062-9.
Amb t 5 - Protein Sequences
Source Link to source
SwissProt P10414
Amb t 5 - PDB Structure
PDB Id PDB Name PDB Entry Deposition Date Experiment Type Observation
9 142 1BBG 24-APR-98 NMR, minimized average structure
9 143 2BBG 24-APR-98 NMR, 30 structures
9 144 3BBG 24-APR-98 NMR, 2 structures
3BBG.pdb


Amb t 5 - Sequence Search
Sequence Header Sequence
Amb t 5
SDAP Sequence ID: 25
SDAP Allergen ID: 9
MKNIFMLTLFILIITSTIKAIGSTNEVDEIKQEDDGLCYEGTNCGKVGKYCCSPIGKYCVCYDSKAICNKNCT
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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Blast NR database search at NCBI
Expasy Blast Search
Amb t 5 - 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
Amb t 5 67.6 0.4 1BBG_A 100 40 73 34 - 73 1 - 40 4.01e-23 83.6 Download (SI: 25)
Amb t 5 - Alphafold Theoretical Model Structure
Model Structure
25_relaxed_rank_1_model_2.pdb


Coverage Plddt
Amb t 5 - Protein Sequence Properties!
Protein Sequence Protease cleavage sites PeptideCutter at ExPASy
P10414 Click here to process the data
Amb t 5 - PFAM Information
SeqID Aller ID AlnS AlnE EnvS EnvE PFAM ID Family Type Clan Description
25 9 36 73 35 73 PF03913 Ragweed_pollen Family No_clan Ragweed group 5 pollen allergen
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 Amb t 5

Probe radius : 1.400

POLAR area/energy = 2293.65

APOLAR area/energy = 4923.89

Total area/energy = 7217.53

Number of surface atoms = 419

Number of buried atoms = 137

Residues Predicted with high probability (in top five patches) are: 53,56,57,58,54,55,36,37,38,39,50,62,65,69,1,40 , and medium probability (next top five patches) are : 40,42,43,48,49,63,64,67,31,32,33,34,35,66,70,71 . Predicted residues are shown in red and green color stick representation.

Original PDB file 972.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. 1972.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
972.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)
972.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
972.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

Amb t 5 - 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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