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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RICIN BOUND WITH FORMYCIN MONOPHOSPHATE

Authors :   A. F. Monzingo, J. D. Robertus

Date :   03 May 11 (Deposition) - 31 Aug 11 (Release) - 31 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Glycosidase, Ribosome-Inactivating Protein, Lectin, Glycoprotein, Lactose Binding, Glycosylation, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. F. Monzingo, J. D. Robertus
X-Ray Analysis Of Substrate Analogs In The Ricin A-Chain Active Site.
J. Mol. Biol. V. 227 1136 1992
PubMed-ID: 1433290

Molecule 1 - RICIN
	Chains	:	A
	EC Number	:	3.2.2.22
	Fragment	:	RICIN A CHAIN
	Organism Common	:	CASTOR BEAN
	Organism Scientific	:	RICINUS COMMUNIS
	Organism Taxid	:	3988
	Other Details	:	SEED
	Synonym	:	RICIN A CHAIN, RRNA N-GLYCOSIDASE, LINKER PEPTIDE, RICIN B CHAIN

Molecule 2 - RICIN
	Chains	:	B
	EC Number	:	3.2.2.22
	Fragment	:	RICIN B CHAIN
	Organism Common	:	CASTOR BEAN
	Organism Scientific	:	RICINUS COMMUNIS
	Organism Taxid	:	3988
	Other Details	:	SEED
	Synonym	:	RICIN A CHAIN, RRNA N-GLYCOSIDASE, LINKER PEPTIDE, RICIN B CHAIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 9)

No.	Name	Count	Type	Full Name
1	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
2	FMP	1	Ligand/Ion	FORMYCIN-5'-MONOPHOSPHATE
3	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
4	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:22 , ASP B:25 , GLN B:35 , TRP B:37 , LYS B:40 , ASN B:46 , BGC B:265	BINDING SITE FOR RESIDUE GAL B 264
2	AC2	SOFTWARE	ASP B:25 , GAL B:264	BINDING SITE FOR RESIDUE BGC B 265
3	AC3	SOFTWARE	GLU B:199 , ASP B:234 , ARG B:236 , ALA B:237 , HIS B:251 , ASN B:255 , BGC B:268	BINDING SITE FOR RESIDUE GAL B 267
4	AC4	SOFTWARE	ALA B:237 , GAL B:267 , HOH B:285	BINDING SITE FOR RESIDUE BGC B 268
5	AC5	SOFTWARE	TRP B:93 , ASN B:95 , TYR B:125 , LEU B:227 , NAG B:271	BINDING SITE FOR RESIDUE NAG B 270
6	AC6	SOFTWARE	TRP B:93 , NAG B:270	BINDING SITE FOR RESIDUE NAG B 271
7	AC7	SOFTWARE	PHE A:226 , ALA A:227 , PRO A:229 , TYR A:243 , ILE B:10 , ASN B:135 , NAG B:281	BINDING SITE FOR RESIDUE NAG B 280
8	AC8	SOFTWARE	THR B:43 , LEU B:48 , NAG B:280	BINDING SITE FOR RESIDUE NAG B 281
9	AC9	SOFTWARE	ALA A:79 , TYR A:80 , VAL A:81 , GLY A:121 , ASN A:122 , TYR A:123 , ILE A:172 , GLU A:177 , ARG A:180 , GLU A:208 , TRP A:211 , HOH A:291	BINDING SITE FOR RESIDUE FMP A 301

Asymmetric/Biological Unit

No.	Residues
1	A:259	-	B:4
2	B:20	-	B:39
3	B:63	-	B:80
4	B:151	-	B:164
5	B:190	-	B:207

(no "Cis Peptide Bond" information available for 3RTI)

(no "SAP(SNP)/Variant" information available for 3RTI)

Asymmetric/Biological Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIGA_RICIN	PS00275	Shiga/ricin ribosomal inactivating toxins active site signature.	RICI_RICCO	207-223	1	A:172-188
2	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	RICI_RICCO	321-448 451-575	2	B:7-134 B:137-261

(no "Exon" information available for 3RTI)

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:257
 aligned with RICI_RICCO | P02879 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:257
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       
           RICI_RICCO    41 YPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPP 297
               SCOP domains d3rtia_ A: Ricin A-chain                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhhhh....ee..ee........hhhh.eeeeeee.....eeeeeee.....eeeeee..eeee....hhhhhhhhh.......eeee.....hhhhhhhhhh........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeee.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      -------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rti A   6 YPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPP 262
                                    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

Chain B from PDB  Type:PROTEIN  Length:259
 aligned with RICI_RICCO | P02879 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:262
                                   324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574  
           RICI_RICCO   315 ADVCMDPEPIVRIVGRNGLCVDVRDGRFHNGNAIQLWPCKSNTDANQLWTLKRDNTIRSNGKCLTTYGYSPGVYVMIYDCNTAATDATRWQIWDNGTIINPRSSLVLAATSGNSGTTLTVQTNIYAVSQGWLPTNNTQPFVTTIVGLYGLCLQANSGQVWIEDCSSEKAEQQWALYADGSIRPQQNRDNCLTSDSNIRETVVKILSCGPASSGQRWMFKNDGTILNLYSGLVLDVRASDPSLKQIILYPLHGDPNQIWLPLF 576
               SCOP domains d3rtib1 B:1-135 Plant cytotoxin B-chain (lectin)                                                                                       d3rtib2 B:136-262 Plant cytotox   in B-chain (lectin)                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee.eehhhhheeee.hhh......eeee......hhhhheee.....eee..eeeee........eeee.....hhhhh..ee.....ee.....eeee..........eeee...hhhhh.ee......eeeeeehhhhheeeee..eeeee....---..eeee.....eee.....eeee..........eeee....hhhhh.ee.....ee......eeee.hhhhhhh.eeee....hhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------RICIN_B_LECTIN  PDB: B:7-134 UniProt: 321-448                                                                                   --RICIN_B_LECTIN  PDB: B:137-261 UniProt: 451-575                                                                              - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rti B   1 ADVCMDPEPIVRIVGRNGLCVDVRDGRFHNGNAIQLWPCKSNTDANQLWTLKRDNTIRSNGKCLTTYGYSPGVYVMIYDCNTAATDATRWQIWDNGTIINPRSSLVLAATSGNSGTTLTVQTNIYAVSQGWLPTNNTQPFVTTIVGLYGLCLQANSGQVWIEDCSS---EQQWALYADGSIRPQQNRDNCLTSDSNIRETVVKILSCGPASSGQRWMFKNDGTILNLYSGLVLDVRASDPSLKQIILYPLHGDPNQIWLPLF 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  
                                                                                                                                                                                               166 170

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 '\|'

(no "CATH Domain" information available for 3RTI, only for superseded entry 1FMP replaced by 3RTI)

(no "Pfam Domain" information available for 3RTI)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RICI_RICCO | P02879)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0031640	killing of cells of other organism	Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
	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:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3rti)

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	3rti
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2aai	THE NATIVE PROTEIN RICIN
3rtj

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (5, 5)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 3)

CATH Domains (0, 0 ; only for superseded entry 1FMP: 2,2)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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