2VS6 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   K173A, R174A, K177A-TRICHOSANTHIN

Authors :   P. H. Too, M. K. Ma, A. N. Mak, C. K. Tung, G. Zhu, S. W. Au, K. B. Wong, P. C. Sh

Date :   21 Apr 08 (Deposition) - 30 Dec 08 (Release) - 28 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Antiviral Protein, Protein Synthesis Inhibitor, Tcs, Toxin, Hydrolase, Plant Defense (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. H. Too, M. K. Ma, A. N. Mak, Y. T. Wong, C. K. Tung, G. Zhu, S. W. Au, K. B. Wong, P. C. Shaw
The C-Terminal Fragment Of The Ribosomal P Protein Complexe To Trichosanthin Reveals The Interaction Between The Ribosome-Inactivating Protein And The Ribosome.
Nucleic Acids Res. V. 37 602 2009
PubMed-ID: 19073700 | Reference-DOI: 10.1093/NAR/GKN922

Molecule 1 - RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN
	Chains	:	A, B
	EC Number	:	3.2.2.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	469008
	Mutation	:	YES
	Organism Common	:	MONGOLIAN SNAKE-GOURD
	Organism Scientific	:	TRICHOSANTHES KIRILOWII
	Organism Taxid	:	3677
	Synonym	:	RRNA N-GLYCOSIDASE, ALPHA-TCS, TRICHOSANTHIN MUTANT K173A, R174A AND K177A

		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 2VS6)

(no "Site" information available for 2VS6)

(no "SS Bond" information available for 2VS6)

(no "Cis Peptide Bond" information available for 2VS6)

(no "SAP(SNP)/Variant" information available for 2VS6)

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.	RIPT_TRIKI	178-194	2	A:155-171 B:155-171

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.	RIPT_TRIKI	178-194	1	A:155-171 -

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.	RIPT_TRIKI	178-194	1	- B:155-171

(no "Exon" information available for 2VS6)

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:247
 aligned with RIPT_TRIKI | P09989 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:247
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       
           RIPT_TRIKI    23 GDVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALLLNRNNM 269
               SCOP domains d2vs6a_ A: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains -2vs6A01 A:1-162 Ricin (A subunit), domain 1                                                                                                                       2vs6A02 A:163-246 Ricin (A Subunit), domain 2                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhhh..eeeee..eeee....hhhhheeeeeee.....eeeeeee.....eeeeee..eeee..hhhhhhhh........eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeee..hhhhhh......hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      --------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vs6 A   0 MDVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGAAVDATFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALLLNRNNM 246
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239

Chain B from PDB  Type:PROTEIN  Length:248
 aligned with RIPT_TRIKI | P09989 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:248
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262        
           RIPT_TRIKI    23 GDVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALLLNRNNMA 270
               SCOP domains d2vs6b_ B: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -2vs6B01 B:1-162 Ricin (A subunit), domain 1                                                                                                                       2vs6B02 B:163-247 Ricin (A Subunit), domain 2                                         CATH domains
           Pfam domains (1) ---RIP-2vs6B01 B:3-202                                                                                                                                                                                     --------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---RIP-2vs6B02 B:3-202                                                                                                                                                                                     --------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeee....hhhhhhhhhhhhhhh..eeeee..eeee....hhhhheeeeeee.....eeeeeee.....eeeeee..eeee..hhhhhhhh........eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeee..hhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ---------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vs6 B   0 MDVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGAAVDATFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALLLNRNNMA 247
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239

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: automated matches (73)

Mongolian snake-gourd (Trichosanthes kirilowii) [TaxId: 3677] (2)

1a	d2vs6a_	A:
1b	d2vs6b_	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)

Mongolian snake-gourd (Trichosanthes kirilowii) (3)

1a	2vs6A01	A:1-162
1b	2vs6B01	B:1-162

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

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

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

Mongolian snake-gourd (Trichosanthes kirilowii) (3)

2a	2vs6A02	A:163-246
2b	2vs6B02	B:163-247

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: RIP] (62)

Family: RIP (62)

Trichosanthes kirilowii (Chinese snake gourd) (Chinese cucumber) (8)

1a	RIP-2vs6B01	B:3-202
1b	RIP-2vs6B02	B:3-202

Asymmetric Unit(hide GO term definitions)

Chain A,B (RIPT_TRIKI | P09989)

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: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.
	GO:0050688	regulation of defense response to virus	Any process that modulates the frequency, rate or extent of the antiviral response of a cell or organism.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
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Biological Units
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		Biological Unit 2	[ Jena3D ]

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Access by PDB/NDB ID
	2vs6
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	RIPT_TRIKI \| P09989
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	3.2.2.22
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		Domain Information	:	XDom
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	RIPT_TRIKI \| P09989
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UniProtKB/Swiss-Prot
	RIPT_TRIKI \| P09989	:	1gis 1giu 1j4g 1mrj 1mrk 1nli 1qd2 1tcs 2jdl 2jjr

1gis	A TRICHOSANTHIN(TCS) MUTANT(E85Q) COMPLEX STRUCTURE WITH 2'-DEOXY- ADENOSIN-5'- MONOPHOSPHATE
1giu	A TRICHOSANTHIN(TCS) MUTANT(E85R) COMPLEX STRUCTURE WITHADENINE
1j4g	CRYSTAL STRUCTURE ANALYSIS OF THE TRICHOSANTHIN DELTA C7
1mrj	ALPHA-TRICHOSANTHIN COMPLEXED WITH ADENINE
1mrk	ALPHA-TRICHOSANTHIN COMPLEXED WITH FORMYCIN
1nli	COMPLEX OF [E160A-E189A] TRICHOSANTHIN AND ADENINE
1qd2	CRYSTAL STRUCTURE OF THE COMPLEX OF TRICHOSANTHIN WITH ADENINE, OBTAINED FROM TRICHOSANTHIN COMPLEXED WITH THE DINUCLEOTIDE APG
1tcs	TRICHOSANTHIN COMPLEXED WITH NADPH
2jdl	STRUCTURE OF C-TERMINAL REGION OF ACIDIC P2 RIBOSOMAL PROTEIN COMPLEXED WITH TRICHOSANTHIN
2jjr	V232K, N236D-TRICHOSANTHIN

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Ligands, Modified Residues, Ions (0, 0)

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Gene Ontology (5, 5)

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