1D6A - JenaLib

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Title :   STRUCTURE OF POKEWEED ANTIVIRAL PROTEIN COMPLEXED WITH GUANINE

Authors :   I. V. Kurinov, F. Rajamohan, T. K. Venkatachalam, F. M. Uckun

Date :   12 Oct 99 (Deposition) - 16 Dec 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Pokeweed Antiviral Protein, Ribosome Inactivating Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. V. Kurinov, F. Rajamohan, T. K. Venkatachalam, F. M. Uckun
X-Ray Crystallographic Analysis Of The Structural Basis For The Interaction Of Pokeweed Antiviral Protein With Guanine Residues Of Ribosomal Rna.
Protein Sci. V. 8 2399 1999
PubMed-ID: 10595542
(for further references see the PDB file header)

Molecule 1 - POKEWEED ANTIVIRAL PROTEIN
	Chains	:	A, B
	EC Number	:	3.2.2.22
	Organism Common	:	AMERICAN POKEWEED
	Organism Scientific	:	PHYTOLACCA AMERICANA
	Organism Taxid	:	3527
	Synonym	:	RRNA N-GLYCOSIDASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	GUN	2	Ligand/Ion	GUANINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GUN	1	Ligand/Ion	GUANINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GUN	1	Ligand/Ion	GUANINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:72 , VAL A:73 , SER A:121 , TYR A:123 , ILE A:171 , GLU A:176 , ARG A:179 , HOH A:1057	BINDING SITE FOR RESIDUE GUN A 901
2	AC2	SOFTWARE	TYR B:72 , VAL B:73 , SER B:121 , TYR B:123 , ILE B:171 , GLU B:176 , ARG B:179 , HOH B:1105	BINDING SITE FOR RESIDUE GUN B 902

Asymmetric Unit

No.	Residues
1	A:34	-	A:259
2	A:85	-	A:106
3	B:34	-	B:259
4	B:85	-	B:106

Asymmetric Unit

No.	Residues
1	Asn A:46	-	Pro A:47
2	Asn B:46	-	Pro B:47

(no "SAP(SNP)/Variant" information available for 1D6A)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIGA_RICIN	PS00275	Shiga/ricin ribosomal inactivating toxins active site signature.	RIP1_PHYAM	193-209	2	A:171-187 B:171-187

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIGA_RICIN	PS00275	Shiga/ricin ribosomal inactivating toxins active site signature.	RIP1_PHYAM	193-209	1	A:171-187 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIGA_RICIN	PS00275	Shiga/ricin ribosomal inactivating toxins active site signature.	RIP1_PHYAM	193-209	1	- B:171-187

(no "Exon" information available for 1D6A)

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
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Chain A from PDB  Type:PROTEIN  Length:262
 aligned with RIP1_PHYAM | P10297 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:262
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282  
           RIP1_PHYAM    23 VNTIIYNVGSTTISKYATFLNDLRNEAKDPSLKCYGIPMLPNTNTNPKYVLVELQGSNKKTITLMLRRNNLYVMGYSDPFETNKCRYHIFNDISGTERQDVETTLCPNANSRVSKNINFDSRYPTLESKAGVKSRSQVQLGIQILDSNIGKISGVMSFTEKTEAEFLLVAIQMVSEAARFKYIENQVKTNFNRAFNPNPKVLNLQETWGKISTAIHDAKNGVLPKPLELVDASGAKWIVLRVDEIKPDVALLNYVGGSCQTT 284
               SCOP domains d1d6aa_ A: Pokeweed antiviral protein alpha                                                                                                                                                                                                                            SCOP domains
               CATH domains 1d6aA01 A:1-178 Ricin (A subunit), domain 1                                                                                                                                       1d6aA02 A:179-259 Ricin (A Subunit), domain 2                                    --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhhh....ee..ee..........eeeeeee.hhh.eeeeeee.....eeeeeeee...eeeeee.....hhhhhhhhhhhh.hhh.eee.......hhhhhhhhh...hhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeehhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      --------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d6a A   1 VNTIIYNVGSTTISKYATFLNDLRNEAKDPSLKCYGIPMLPNTNTNPKYVLVELQGSNKKTITLMLRRNNLYVMGYSDPFETNKCRYHIFNDISGTERQDVETTLCPNANSRVSKNINFDSRYPTLESKAGVKSRSQVQLGIQILDSNIGKISGVMSFTEKTEAEFLLVAIQMVSEAARFKYIENQVKTNFNRAFNPNPKVLNLQETWGKISTAIHDAKNGVLPKPLELVDASGAKWIVLRVDEIKPDVALLNYVGGSCQTT 262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with RIP1_PHYAM | P10297 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:262
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282  
           RIP1_PHYAM    23 VNTIIYNVGSTTISKYATFLNDLRNEAKDPSLKCYGIPMLPNTNTNPKYVLVELQGSNKKTITLMLRRNNLYVMGYSDPFETNKCRYHIFNDISGTERQDVETTLCPNANSRVSKNINFDSRYPTLESKAGVKSRSQVQLGIQILDSNIGKISGVMSFTEKTEAEFLLVAIQMVSEAARFKYIENQVKTNFNRAFNPNPKVLNLQETWGKISTAIHDAKNGVLPKPLELVDASGAKWIVLRVDEIKPDVALLNYVGGSCQTT 284
               SCOP domains d1d6ab_ B: Pokeweed antiviral protein alpha                                                                                                                                                                                                                            SCOP domains
               CATH domains 1d6aB01 B:1-178 Ricin (A subunit), domain 1                                                                                                                                       1d6aB02 B:179-259 Ricin (A Subunit), domain 2                                    --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhhh....ee..ee..........eeeeeee.hhh.eeeeeee.....eeeeeeee...eeeeee.....hhhhhhhhhhhh.hhh.eee.......hhhhhhhhh...hhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeehhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      --------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d6a B   1 VNTIIYNVGSTTISKYATFLNDLRNEAKDPSLKCYGIPMLPNTNTNPKYVLVELQGSNKKTITLMLRRNNLYVMGYSDPFETNKCRYHIFNDISGTERQDVETTLCPNANSRVSKNINFDSRYPTLESKAGVKSRSQVQLGIQILDSNIGKISGVMSFTEKTEAEFLLVAIQMVSEAARFKYIENQVKTNFNRAFNPNPKVLNLQETWGKISTAIHDAKNGVLPKPLELVDASGAKWIVLRVDEIKPDVALLNYVGGSCQTT 262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

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: Ribosome inactivating proteins (RIP) (180)

Superfamily: Ribosome inactivating proteins (RIP) (180)

Family: Plant cytotoxins (166)

Protein domain: Pokeweed antiviral protein alpha (7)

Pokeweed (Phytolacca americana) [TaxId: 3527] (7)

1a	d1d6aa_	A:
1b	d1d6ab_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Ricin (A subunit); domain 1 (112)

Homologous Superfamily: Ricin (A subunit), domain 1 (112)

American pokeweed (Phytolacca americana) (12)

1a	1d6aA01	A:1-178
1b	1d6aB01	B:1-178

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: Ricin (A Subunit), domain 2 (112)

Homologous Superfamily: Ricin (A Subunit), domain 2 (112)

American pokeweed (Phytolacca americana) (12)

2a	1d6aA02	A:179-259
2b	1d6aB02	B:179-259

(no "Pfam Domain" information available for 1D6A)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RIP1_PHYAM | P10297)

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.

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