1J4G - JenaLib

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Title :   CRYSTAL STRUCTURE ANALYSIS OF THE TRICHOSANTHIN DELTA C7

Authors :   Y. Ding, H. M. Too, Z. L. Wang, Y. W. Liu, Y. C. Dong, P. C. Shaw, Z. H. Rao

Date :   30 Sep 01 (Deposition) - 24 Oct 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

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

Reference :   Y. Ding, H. M. Too, Z. L. Wang, Y. W. Liu, Y. C. Dong, P. C. Shaw, Z. H. Rao
Crystal Structure Analysis Of The Trichosanthin Delta C7
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - TRICHOSANTHIN DELTA C7
	Chains	:	A, B, C, D
	EC Number	:	3.2.2.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET8C
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	TRICHOSANTHES KIRILOWII
	Organism Taxid	:	3677
	Synonym	:	RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH B:1232 , HOH B:1252 , HOH B:1301 , HOH B:1307 , HOH B:1316	BINDING SITE FOR RESIDUE CA B 1201
2	AC2	SOFTWARE	HOH A:1332 , HOH A:1335 , HOH A:1343 , HOH A:1346 , HOH A:1379	BINDING SITE FOR RESIDUE CA A 1202
3	AC3	SOFTWARE	HOH D:1225 , HOH D:1339 , HOH D:1345 , HOH D:1362	BINDING SITE FOR RESIDUE CA D 1203
4	AC4	SOFTWARE	LEU C:240 , HOH C:1277 , HOH C:1372	BINDING SITE FOR RESIDUE CA C 1204

(no "SS Bond" information available for 1J4G)

(no "Cis Peptide Bond" information available for 1J4G)

(no "SAP(SNP)/Variant" information available for 1J4G)

Asymmetric Unit (1, 4)

	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	4	A:155-171 B:155-171 C:155-171 D: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 - -

Biological Unit 3 (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	- - C:155-171 -

Biological Unit 4 (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	- - - D:155-171

(no "Exon" information available for 1J4G)

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:241
 aligned with RIPT_TRIKI | P09989 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:241
                                    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 GDVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALL 263
               SCOP domains d1j4ga_ A: alpha-Trichosanthin                                                                                                                                                                                                                    SCOP domains
               CATH domains -1j4gA01 A:1-162 Ricin (A subunit), domain 1                                                                                                                       1j4gA02 A:163-240 Ricin (A Subunit), domain 2                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....hhhhhhhhhhhhhhh..eeeee..eeee....hhhhheeeeeee.....eeeeeee.....eeeeee..eeee..hhhhhhhhhhh.....eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee..hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      --------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j4g A   0 MDVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALL 240
                                     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:241
 aligned with RIPT_TRIKI | P09989 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:241
                                    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 GDVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALL 263
               SCOP domains d1j4gb_ B: alpha-Trichosanthin                                                                                                                                                                                                                    SCOP domains
               CATH domains -1j4gB01 B:1-162 Ricin (A subunit), domain 1                                                                                                                       1j4gB02 B:163-240 Ricin (A Subunit), domain 2                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhhhh.eeeee..eeee....hhhhheeeeeee.....eeeeeee.....eeeeee..eeee..hhhhhhhh........eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeee..hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      --------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j4g B   0 MDVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALL 240
                                     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 C from PDB  Type:PROTEIN  Length:241
 aligned with RIPT_TRIKI | P09989 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:241
                                    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 GDVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALL 263
               SCOP domains d1j4gc_ C: alpha-Trichosanthin                                                                                                                                                                                                                    SCOP domains
               CATH domains -1j4gC01 C:1-162 Ricin (A subunit), domain 1                                                                                                                       1j4gC02 C:163-240 Ricin (A Subunit), domain 2                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....hhhhhhhhhhhhhhh..eeeee..eeee....hhhhheeeeeee.....eeeeeee.....eeeeee..eeeee.hhhhhhhhhhh.....eeeee....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee..hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      --------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j4g C   0 MDVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALL 240
                                     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 D from PDB  Type:PROTEIN  Length:241
 aligned with RIPT_TRIKI | P09989 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:241
                                    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 GDVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALL 263
               SCOP domains d1j4gd_ D: alpha-Trichosanthin                                                                                                                                                                                                                    SCOP domains
               CATH domains -1j4gD01 D:1-162 Ricin (A subunit), domain 1                                                                                                                       1j4gD02 D:163-240 Ricin (A Subunit), domain 2                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhhhh.eeeee..eeee....hhhhheeeeeee.....eeeeeee.....eeeeee..eeee..hhhhhhhh........eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeee..hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      --------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j4g D   0 MDVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALL 240
                                     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: alpha-Trichosanthin (9)

Mongolian snake gourd (Trichosanthes kirilowii Maxim.) [TaxId: 3677] (9)

1a	d1j4ga_	A:
1b	d1j4gb_	B:
1c	d1j4gc_	C:
1d	d1j4gd_	D:

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)

Trichosanthes kirilowii. Organism_taxid: 3677. (3)

1a	1j4gA01	A:1-162
1b	1j4gB01	B:1-162
1c	1j4gC01	C:1-162
1d	1j4gD01	D: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)

Trichosanthes kirilowii. Organism_taxid: 3677. (3)

2a	1j4gA02	A:163-240
2b	1j4gB02	B:163-240
2c	1j4gC02	C:163-240
2d	1j4gD02	D:163-240

(no "Pfam Domain" information available for 1J4G)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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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(no "Related Entries Specified in the PDB File" available for 1J4G)

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