1APA - JenaLib

Title :   X-RAY STRUCTURE OF A POKEWEED ANTIVIRAL PROTEIN, CODED BY A NEW GENOMIC CLONE, AT 0.23 NM RESOLUTION. A MODEL STRUCTURE PROVIDES A SUITABLE ELECTROSTATIC FIELD FOR SUBSTRATE BINDING.

Authors :   H. Ago, J. Kataoka, H. Tsuge, N. Habuka, E. Inagaki, M. Noma, M. Miyano

Date :   21 Sep 93 (Deposition) - 31 Jan 94 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

Keywords :   Antiviral Protein, Genomic Clone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Ago, J. Kataoka, H. Tsuge, N. Habuka, E. Inagaki, M. Noma, M. Miyano
X-Ray Structure Of A Pokeweed Antiviral Protein, Coded By A New Genomic Clone, At 0. 23 Nm Resolution. A Model Structure Provides A Suitable Electrostatic Field For Substrate Binding.
Eur. J. Biochem. V. 225 369 1994
PubMed-ID: 7925458 | Reference-DOI: 10.1111/J.1432-1033.1994.00369.X
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:261
 aligned with RIPA_PHYAM | Q03464 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:261
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284 
           RIPA_PHYAM    25 INTITFDVGNATINKYATFMKSIHNQAKDPTLKCYGIPMLPNTNLTPKYLLVTLQDSSLKTITLMLKRNNLYVMGYADTYNGKCRYHIFKDISNTTERNDVMTTLCPNPSSRVGKNINYDSSYPALEKKVGRPRSQVQLGIQILNSGIGKIYGVDSFTEKTEAEFLLVAIQMVSEAARFKYIENQVKTNFNRAFYPNAKVLNLEESWGKISTAIHNAKNGALTSPLELKNANGSKWIVLRVDDIEPDVGLLKYVNGTCQAT 285
               SCOP domains d1apaa_ A: Pokeweed antiviral protein alpha                                                                                                                                                                                                                           SCOP domains
               CATH domains 1apaA01 A:6-182 Ricin (A subunit), domain 1                                                                                                                                      1apaA02 A:183-263 Ricin (A Subunit), domain 2                                    --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....hhhhhhhhhhhhhhh.....................eeeeeee.....eeeeeee.....eeeeeee....eeeeee.....hhhhhhhhhhh......eee........hhhhhhhh..........hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhh.........hhhhhhhhhhhhhhhhhhh.........eeee.....eeee..hhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1apa A   6 INTITFDVGNATINKYATFMKSIHNQAKDPTLKCYGIPMLPNTNLTPKYLLVTLQDSSLKTITLMLKRNNLYVMGYADTYNGKCRYHIFKDISNTTERNDVMTTLCPNPSSRVGKNINYDSSYPALEKKVGRPRSQVQLGIQILNSGIGKIYGVDSFTEKTEAEFLLVAIQMVSEAARFKYIENQVKTNFNRAFYPNAKVLNLEESWGKISTAIHNAKNGALTSPLELKNANGSKWIVLRVDDIEPDVGLLKYVNGTCQAT 266
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RIPA_PHYAM | Q03464)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0030598	rRNA N-glycosylase activity	Catalysis of the hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes or corresponding sites in 28S RNA from other species.
biological process
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0017148	negative regulation of translation	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	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.

Visualization

Interactive Views

Asymmetric/Biological 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 1apa)

	Sites
(no "Sites" information available for 1apa)

	Cis Peptide Bonds
		Thr A:51 - Pro A:52	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1apa
		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
	RIPA_PHYAM \| Q03464
		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

Description