The University of Texas Medical Branch
Department of Biochemistry and Molecular Biology Sealy Center for Structural Biology Computational Biology



SDAP Home Page
SDAP Overview

Use SDAP
SDAP All
SDAP Food

SDAP Tools
FAO/WHO Allergenicity Test
FASTA Search in SDAP
Peptide Match
Peptide Similarity
Peptide-Protein PD Index
Aller_ML, Allergen Markup Language
List SDAP

About SDAP
General Information
Manual
FAQ
Publications
Who Are We
Advisory Board

Allergy Links

Our Software Tools
MPACK
FANTOM
GETAREA
InterProSurf
EpiSearch

Allergen Databases
WHO/IUIS Allergen Nomenclature database
FARRP Allergen Protein Database (University of Nebraska)
Allergen Database for Food Safety (ADFS)
COMPARE database
ALLFAM (Medical University of Vienna)
Allermatch (Wageninen University)

Protein Databases
PDB
MMDB - Entrez
SWISS-PROT
NCBI - Entrez
PIR

Protein Classification
CATH
FSSP
iProClass
ProtoMap
SCOP
VAST

Bioinformatics Servers
BLAST @ NCBI
FASTA @ EMBL-EBI
Peptide Match @ PIR
ClustalW @ EMBL - EBI


                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 1566
Allergen Scientific Name Amb a 11.0101
Allergen Species - Systematic Name Ambrosia artemisiifolia
Allergen Species - Common Name short ragweed
Allergen Common source weed
Allergen Common name Asterales
Allergen Keywords Cysteine protease
Allergen IUIS (Yes=1, No=0) 1
Amb a 11.0101 - References
ID Reference
Pubmed ID: 25865353
Bouley J, Groeme R, Le Mignon M, Jain K, Chabre H, Bordas-Le Floch V, Couret MN, Bussières L, Lautrette A, Naveau M, Baron-Bodo V, Lombardi V, Mascarell L, Batard T, Nony E, Moingeon P. Identification of the cysteine protease Amb a 11 as a novel major allergen from short ragweed. J Allergy Clin Immunol. 2015 Oct;136(4):1055-64. doi: 10.1016/j.jaci.2015.03.001. Epub 2015 Apr 10. PMID: 25865353.
Amb a 11.0101 - Protein Sequences
Source Link to source
GenBank V5LU01
Amb a 11.0101 - PDB Structure
PDB Id PDB Name PDB Entry Deposition Date Experiment Type Observation
1566 308 5EGW 2016-04-27 X-ray diffraction resolution 2.7 A A crystal structure of the Amb a 11 cysteine protease, a major ragweed pollen allergen, in its proform.
1566 309 5EF4 2016-04-27 X-ray diffraction resolution 2.05 A A crystal structure of the Amb a 11 cysteine protease, a major ragweed pollen allergen, in its proform.
5EF4.pdb


Amb a 11.0101 - Sequence Search
Sequence Header Sequence
Amb a 11.0101
SDAP Sequence ID: 1344
SDAP Allergen ID: 1566
MEINKLVCFSFSLVLILGLVESFHYHERELESEEGFMGMYDRWREQHNIEMRSPERFNVFKYNVRRIHESNKMDKPYKLKVNEFADMTNLEFVNTYANSKISHFQALRGSAPGSIDTDPNKDFIYANVTKIPDKVDWREKNAVTDVKGQGGCGSCWAFAAVVALEGINAIRTGKLVKFSEQQLVDCDMTNAGCDGGLMEPAFTYVIKHGGIAPEASYPYVGKRETCDKAKIKDVLKIDGRQNVPGLDEEALRKAVAHQPVATGIQLSGHGLQFYSEGVYTGDCGTEPNHGVGIVGYGENEKGIKFWTVKNSWGPTWGEKGYIHLQRGARKEGLCGVAMHSSFPIMNDPNPPKDDPNGPKDDPDAPKDPKFKTTQRLQGIRTKLLEL
View 3D Structure Click here to view 3D model structure of allergen
Fasta Search in SDAP
Blast Swissprot database search at NCBI
Blast PDB database search at NCBI
Blast NR database search at NCBI
Expasy Blast Search
Amb a 11.0101 - 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 a 11.0101 92.3 0.8 5EF4_A 100 364 386 23 - 386 22 - 385 0 766 Download (SI: 1344)
Amb a 11.0101 - Alphafold Theoretical Model Structure
Model Structure
1344_relaxed_rank_1_model_1.pdb


Coverage Plddt
Amb a 11.0101 - Protein Sequence Properties!
Protein Sequence Protease cleavage sites PeptideCutter at ExPASy
V5LU01 Click here to process the data
Amb a 11.0101 - PFAM Information
SeqID Aller ID AlnS AlnE EnvS EnvE PFAM ID Family Type Clan Description
1344 1566 41 92 40 92 PF08246 Inhibitor_I29 Domain No_clan Cathepsin propeptide inhibitor domain (I29)
1344 1566 131 344 131 344 PF00112 Peptidase_C1 Domain CL0125 Papain family cysteine protease
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 a 11.0101

Probe radius : 1.400

POLAR area/energy = 7650.28

APOLAR area/energy = 13334.70

Total area/energy = 20984.97

Number of surface atoms = 1706

Number of buried atoms = 1330

Residues Predicted with high probability (in top five patches) are: 22,23,24,25,26,46,47,80,96,148,150,312,313,188,189,190,200,203 , and medium probability (next top five patches) are : 203,73,74,75,27,28,29,70,76,77,78,280,281,30,206,207,208,209,186 . Predicted residues are shown in red and green color stick representation.

Original PDB file 373.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. 1373.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
373.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)
373.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
373.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 a 11.0101 - 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!
SDAP Home Page | Search SDAP | SDAP Manual | SDAP FAQ | Contact  
UTMB | Search | Directories | UTMB Map | News | Employment | Sitemap 
This site published by Surendra Negi
Copyright   2001-2022  The University of Texas Medical Branch. Please review our privacy policy and Internet guidelines.