2VZN - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE MAJOR ALLERGEN FROM FIRE ANT VENOM, SOL I 3

Authors :   S. Padavattan, Z. Markovic-Housley

Date :   05 Aug 08 (Deposition) - 09 Sep 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.05

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Major Fire Ant Allergen, Sol I 3, Secreted, Allergen, Cross- Reactivity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Padavattan, M. Schmidt, D. R. Hoffman, Z. Markovic-Housley
Crystal Structure Of The Major Allergen From Fire Ant Venom, Sol I 3
J. Mol. Biol. V. 383 178 2008
PubMed-ID: 18761353 | Reference-DOI: 10.1016/J.JMB.2008.08.023

Molecule 1 - VENOM ALLERGEN 3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF9
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Organism Common	:	RED FIRE ANT
	Organism Scientific	:	SOLENOPSIS INVICTA
	Organism Taxid	:	13686
	Synonym	:	VENOM ALLERGEN III, ALLERGEN SOL I III, VENOM ALLERGEN SOLI 3
	Tissue	:	VENOM GLAND

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2VZN)

(no "Site" information available for 2VZN)

Asymmetric Unit

No.	Residues
1	A:4	-	A:19
2	A:30	-	A:96
3	A:176	-	A:194
4	B:4	-	B:19
5	B:30	-	B:96
6	B:176	-	B:194

Asymmetric Unit

No.	Residues
1	Gly A:197	-	Pro A:198
2	Gly B:197	-	Pro B:198

(no "SAP(SNP)/Variant" information available for 2VZN)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRISP_1	PS01009	CRISP family signature 1.	VA3_SOLIN	183-193	2	A:161-171 B:161-171
2	CRISP_2	PS01010	CRISP family signature 2.	VA3_SOLIN	213-224	2	A:191-202 B:191-202

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRISP_1	PS01009	CRISP family signature 1.	VA3_SOLIN	183-193	1	A:161-171 -
2	CRISP_2	PS01010	CRISP family signature 2.	VA3_SOLIN	213-224	1	A:191-202 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRISP_1	PS01009	CRISP family signature 1.	VA3_SOLIN	183-193	1	- B:161-171
2	CRISP_2	PS01010	CRISP family signature 2.	VA3_SOLIN	213-224	1	- B:191-202

(no "Exon" information available for 2VZN)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:216
 aligned with VA3_SOLIN | P35778 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:217
                                                                                                                                                                                                                                            234      
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233|      
            VA3_SOLIN    24 NYCNLQSCKRNNAIHTMCQYTSPTPGPMCLEYSNVGFTDAEKDAIVNKHNELRQRVASGKEMRGTNGPQPPAVKMPNLTWDPELATIAQRWANQCTFEHDACRNVERFAVGQNIAATSSSGKNKSTPNEMILLWYNEVKDFDNRWISSFPSDDNILMKVGHYTQIVWAKTTKIGCGRIMFKEPDNWTKHYLVCNYGPAGNVLGAPIYEIKK------   -
               SCOP domains d2vzna_ A: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh...hhhhhh...........ee....hhhhhhhhhhhhhhhhhhhhh....................eehhhhhhhhhhhhh.................eeeeeeeee..-...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....eeeeeeeeee.....eeeeeeeeee..................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------CRISP_1    -------------------CRISP_2     ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vzn A   2 NYCNLQSCKRNNAIHTMCQYTSPTPGPMCLEYSNVGFTDAEKDAIVNKHNELRQRVASGKEMRGTNGPQPPAVKMPNLTWDPELATIAQRWANQCTFEHDACRNVERFAVGQNIAATSSSG-NKSTPNEMILLWYNEVKDFDNRWISSFPSDDNILMKVGHYTQIVWAKTTKIGCGRIMFKEPDNWTKHYLVCNYGPAGNVLGAPIYEIKKHHHHHH 218
                                    11        21        31        41        51        61        71        81        91       101       111       121| |    131       141       151       161       171       181       191       201       211       
                                                                                                                                                  122 |                                                                                              
                                                                                                                                                    124

Chain B from PDB  Type:PROTEIN  Length:204
 aligned with VA3_SOLIN | P35778 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:215
                                                                                                                                                                                                                                            234    
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233|    
            VA3_SOLIN    24 NYCNLQSCKRNNAIHTMCQYTSPTPGPMCLEYSNVGFTDAEKDAIVNKHNELRQRVASGKEMRGTNGPQPPAVKMPNLTWDPELATIAQRWANQCTFEHDACRNVERFAVGQNIAATSSSGKNKSTPNEMILLWYNEVKDFDNRWISSFPSDDNILMKVGHYTQIVWAKTTKIGCGRIMFKEPDNWTKHYLVCNYGPAGNVLGAPIYEIKK----   -
               SCOP domains d2v  zn     b_ B: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---  --     ---------------------------------CAP-2vznB01 B:47-196                                                                                                                                  -------------------- Pfam domains (1)
           Pfam domains (2) ---  --     ---------------------------------CAP-2vznB02 B:47-196                                                                                                                                  -------------------- Pfam domains (2)
         Sec.struct. author ...--..-----..hhhhhh.....hhhhheee....hhhhhhhhhhhhhhhhhhhhh....................eehhhhhhhhhhhhh.................eeeeeeeee.---..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....eeeeeeeeee.-...eeeeeeeeee................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------CRISP_1    -------------------CRISP_2     -------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vzn B   2 NYC--QS-----AIHTMCQYTSPTPGPMCLEYSNVGFTDAEKDAIVNKHNELRQRVASGKEMRGTNGPQPPAVKMPNLTWDPELATIAQRWANQCTFEHDACRNVERFAVGQNIAATSSS---KSTPNEMILLWYNEVKDFDNRWISSFPSDDNILMKVGHYTQIVWAKTTKIGCGRIMFKE-DNWTKHYLVCNYGPAGNVLGAPIYEIKKHHHH 216
                              |  ||  -  |     21        31        41        51        61        71        81        91       101       111       121   |   131       141       151       161       171       181 | |   191       201       211     
                              4  7|    14                                                                                                        121 125                                                       183 |                               
                                  8                                                                                                                                                                              185

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: PR-1-like (14)

Superfamily: PR-1-like (14)

Family: automated matches (4)

Protein domain: automated matches (4)

Red fire ant (Solenopsis invicta) [TaxId: 13686] (1)

1a	d2vzna_	A:
1b	d2vznb_	B:

(no "CATH Domain" information available for 2VZN)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: CAP] (7)

Family: CAP (7)

Solenopsis invicta (Red imported fire ant) (Solenopsis wagneri) (1)

1a	CAP-2vznB01	B:47-196
1b	CAP-2vznB02	B:47-196

Asymmetric Unit(hide GO term definitions)

Chain A,B (VA3_SOLIN | P35778)

cellular component
	GO:0005576		extracellular region		The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2vzn)

	Sites
(no "Sites" information available for 2vzn)

	Cis Peptide Bonds
		Gly A:197 - Pro A:198	[ RasMol ]
		Gly B:197 - Pro B:198	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2vzn
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	VA3_SOLIN \| P35778
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	VA3_SOLIN \| P35778
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 2VZN)

(no "Related Entries Specified in the PDB File" available for 2VZN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (1, 1)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File