1IL5 - JenaLib

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Title :   STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 2,5-DIAMINO-4,6-DIHYDROXYPYRIMIDINE (DDP)

Authors :   D. J. Miller, K. Ravikumar, H. Shen, J. -K. Suh, S. M. Kerwin, J. D. Robertus

Date :   07 May 01 (Deposition) - 16 Jan 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Structure-Based Design, Toxin-Inhibitor Complex, Glycosidase, Hydrolase, Ribosome-Inhibiting Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. J. Miller, K. Ravikumar, H. Shen, J. K. Suh, S. M. Kerwin, J. D. Robertus
Structure-Based Design And Characterization Of Novel Platforms For Ricin And Shiga Toxin Inhibition.
J. Med. Chem. V. 45 90 2002
PubMed-ID: 11754581 | Reference-DOI: 10.1021/JM010186S
(for further references see the PDB file header)

Molecule 1 - RICIN A CHAIN
	Chains	:	A, B
	EC Number	:	3.2.2.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	CASTOR BEAN
	Organism Scientific	:	RICINUS COMMUNIS
	Organism Taxid	:	3988

		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, 1)

No.	Name	Count	Type	Full Name
1	DDP	1	Ligand/Ion	2,4-DIAMINO-4,6-DIHYDROXYPYRIMIDINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	DDP	1	Ligand/Ion	2,4-DIAMINO-4,6-DIHYDROXYPYRIMIDINE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	DDP	-1	Ligand/Ion	2,4-DIAMINO-4,6-DIHYDROXYPYRIMIDINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:78 , TYR A:80 , ASN A:122 , TYR A:123 , ARG A:180	BINDING SITE FOR RESIDUE DDP A 301

(no "SS Bond" information available for 1IL5)

(no "Cis Peptide Bond" information available for 1IL5)

(no "SAP(SNP)/Variant" information available for 1IL5)

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.	RICI_RICCO	207-223	2	A:172-188 B:172-188

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.	RICI_RICCO	207-223	1	A:172-188 -

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.	RICI_RICCO	207-223	1	- B:172-188

(no "Exon" information available for 1IL5)

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:264
 aligned with RICI_RICCO | P02879 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:267
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       
           RICI_RICCO    36 IFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPSSQF 302
               SCOP domains d1il5a_ A: Ricin A-chain                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1il5A01 A:1-179 Ricin (A subunit), dom ain 1                                                                                                                                       1il5A02 A:180-263 Ricin (A Subunit), domain 2                                         -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....hhhhhhhhhhhhhhhhh.....-....ee......hhhh.eeeeeee.....eeeeeee.....eeeeee..eeee....hhhhhhhhh.......eeee.....hhhhhhhhhh........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeee.hhhh.....ee.......--.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1il5 A   1 IFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADV-HEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPP--QF 267
                                    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  |  | 
                                                                38 |                                                                                                                                                                                                                            263  | 
                                                                  40                                                                                                                                                                                                                               266

Chain B from PDB  Type:PROTEIN  Length:267
 aligned with RICI_RICCO | P02879 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:267
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       
           RICI_RICCO    36 IFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPSSQF 302
               SCOP domains d1il5b_ B: Ricin A-chain                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1il5B01 B:1-179 Ricin (A subunit), domain 1                                                                                                                                        1il5B02 B:180-267 Ricin (A Subunit), domain 2                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....hhhhhhhhhhhhhhhhh....ee..ee........hhhh.eeeeeee.....eeeeeee.....eeeeee..eeee....hhhhhhhhh.......eeee.....hhhhhhhhhh........hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeee.hhhh.................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1il5 B   1 IFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPSSQF 267
                                    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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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: Ricin A-chain (36)

Castor bean (Ricinus communis) [TaxId: 3988] (36)

1a	d1il5a_	A:
1b	d1il5b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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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)

Castor bean (Ricinus communis) (28)

1a	1il5A01	A:1-179
1b	1il5B01	B:1-179

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

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

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

Castor bean (Ricinus communis) (28)

2a	1il5A02	A:180-263
2b	1il5B02	B:180-267

(no "Pfam Domain" information available for 1IL5)

Asymmetric 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).

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1br5	RICIN A CHAIN (RECOMBINANT) COMPLEX WITH NEOPTERIN
1br6	RICIN A CHAIN (RECOMBINANT) COMPLEX WITH PTEROIC ACID
1fmp	X-RAY ANALYSIS OF SUBSTRATE ANALOGS IN THE RICIN A-CHAIN ACTIVE SITE
1il3	STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 7- DEAZAGUANINE
1il4	STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 9- DEAZAGUANINE
1il9	STRUCTURE OF RICIN A CHAIN BOUND WITH INHIBITOR 8-METHYL-9- OXOGUANINE
1rtc	STRUCTURE OF RECOMBINANT RICIN A CHAIN AT 2.3 A

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