AMPDB_814 | Big defensin

1 General Description

AMPDB ID: AMPDB_814

Protein Names: Big defensin

Protein Family: Big defensin family

Gene Name: Nil

Source Organism: Tachypleus tridentatus (Japanese horseshoe crab)

Protein Length: 117 AA

Protein Existence: Evidence at protein level

2 Protein Sequence & Composition

MKGNIGIAVFYMLLLLLPTDSIGKKMEEEQEKLFRQKRNPLIPAIYIGATVGPSVWAYLVALVGAAAVTAANIRRASSDNHSCAGNRGWCRSKCFRHEYVDTYYSAVCGRYFCCRSR

FASTA format

Counts of Amino Acids

'A': 13, 'R': 10, 'N': 5, 'D': 3, 'C': 6, 'Q': 2, 'E': 5, 'G': 9, 'H': 2, 'I': 7, 'L': 9, 'K': 6, 'M': 3, 'F': 4, 'P': 4, 'S': 8, 'T': 4, 'W': 2, 'Y': 7, 'V': 8

Frequencies of Amino Acids

'A': 11.11%, 'R': 8.55%, 'N': 4.27%, 'D': 2.56%, 'C': 5.13%, 'Q': 1.71%, 'E': 4.27%, 'G': 7.69%, 'H': 1.71%, 'I': 5.98%, 'L': 7.69%, 'K': 5.13%, 'M': 2.56%, 'F': 3.42%, 'P': 3.42%, 'S': 6.84%, 'T': 3.42%, 'W': 1.71%, 'Y': 5.98%, 'V': 6.84%

Missing Amino Acid(s)

No Amino Acid(s) are missing in this protein

Most Occurring Amino Acid(s)

Less Occurring Amino Acid(s)

H, Q, W

Hydrophobic Amino Acid(s) Count

Hydrophilic Amino Acid(s) Count

Basic Amino Acid(s) Count

Acidic Amino Acid(s) Count

Modified Amino Acid(s) Count

Modified Amino Acid(s) Frequencies

Computed by biopython (version 1.79) & proteinAnalysis (version 1)

3 Physicochemical Properties

Sl. No.	Properties	Values	Reference
1.	Molecular Mass	13087.2 Da	Computed by ProtParam module (biopython 1.79)
2.	Aliphatic Index	84.274	Computed by ProtParam module (biopython 1.79)
3.	Instability Index (Half Life)	56.233	Computed by ProtParam module (biopython 1.79)
4.	Hydrophobicity (GRAVY)	-0.024	Computed by ProtParam module (biopython 1.79)
5.	Hydrophobic Moment	0.579	Computed by ProtParam module (biopython 1.79)
6.	Isoelectric Point	9.491	Computed by ProtParam module (biopython 1.79)
7.	Charge (at pH 7)	7.81	Computed by ProtParam module (biopython 1.79)
8.	Secondary Structure Fraction	0.316, 0.222, 0.256 [Helix, Turn, Sheet]	Computed by ProtParam module (biopython 1.79)
9.	Aromaticity	0.111	Computed by ProtParam module (biopython 1.79)
10.	Molar Extinction Coefficient (cysteine\|cystine)	21430, 21805	Computed by ProtParam module (biopython 1.79)

4.1 Target Organism(s)

Gram Negative Bacteria and Gram Positive Bacteria

4.2 Antimicrobial Activity

Antibiotic, Antimicrobial, Defensin, Fungicide, Anti-gram-negative, Anti-gram-Positive

4.3 Enzymatic Activity

4.4 Inhibitory Effect

4.5 Other Biological Activity

Non-hemolytic, Non-ribosomal

Activity data manually curated from Literature and UniProt

5 Database Cross-references

5.1 Literature Database

Citation 1: Kawabata S, Saito T, Saeki K, et al. cDNA cloning, tissue distribution, and subcellular localization of horseshoe crab big defensin. Biol Chem. 1997;378(3-4):289-92. Published 1997 Mar-Apr. doi:10.1515/bchm.1997.378.3-4.289

PMID: 9165083

Citation 2: Saito T, Kawabata S, Shigenaga T, et al. A novel big defensin identified in horseshoe crab hemocytes: isolation, amino acid sequence, and antibacterial activity. J Biochem. 1995;117(5):1131-7. Published 1995 May. doi:10.1093/oxfordjournals.jbchem.a124818

PMID: 8586631

Citation 3: Shigenaga T, Takayenoki Y, Kawasaki S, et al. Separation of large and small granules from horseshoe crab (Tachypleus tridentatus) hemocytes and characterization of their components. J Biochem. 1993;114(3):307-16. Published 1993 Sep. doi:10.1093/oxfordjournals.jbchem.a124173

PMID: 8282718

Citation 4: Agarwala KL, Kawabata Si, Miura Y, et al. Limulus intracellular coagulation inhibitor type 3. Purification, characterization, cDNA cloning, and tissue localization. J Biol Chem. 1996;271(39):23768-74. Published 1996 Sep 27. doi:10.1074/jbc.271.39.23768

PMID: 8798603

Citation 5: Kouno T, Fujitani N, Mizuguchi M, et al. A novel beta-defensin structure: a potential strategy of big defensin for overcoming resistance by Gram-positive bacteria. Biochemistry. 2008;47(40):10611-9. Published 2008 Oct 7. doi:10.1021/bi800957n

PMID: 18785751

5.2 Protein Sequence Databases

5.3 3D Structure Databases

	Sl. no.	PDB ID	Method	Resolution	Access Links	3D View

AlphaFoldDB: P80957

5.4 Nucleotide Sequence Databases

No entries found in GenBank or EMBL

RefSeq: Not found

5.5 Protein-Protein Interaction Databases

STRING: Not found

IntAct: Not found

BioGRID: Not found

5.6 Ligand Databases

BindingDB: Not found

DrugBank: Not found

ChEMBL: Not found

5.7 Family & Domain Databases

InterPro: IPR028060, IPR042033, IPR023355

PANTHER: Not found

PROSITE: Not found

5.8 Genome Annotation Databases

Ensembl: Not found

5.9 Phylogenomic Databases

GeneTree: Not found

5.10 Enzyme & Pathway Databases

BRENDA: Not found

BioCyc: Not found

5.11 Protein-RNA Interaction Databases

RNAct: Not found

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