2Q3N - JenaLib

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Title :   AGGLUTININ FROM ABRUS PRECATORIUS (APA-I)

Authors :   A. Bagaria, K. Surendranath, U. A. Ramagopal, S. Ramakumar, A. A. Karan

Date :   30 May 07 (Deposition) - 26 Jun 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.50

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

Keywords :   Ribosome-Inactivating Protein, Immunotoxin, Agglutinin Abrin, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Bagaria, K. Surendranath, U. A. Ramagopal, S. Ramakumar, A. A. Karande
Structure-Function Analysis And Insights Into The Reduced Toxicity Of Abrus Precatorius Agglutinin I In Relation To Abrin.
J. Biol. Chem. V. 281 34465 2006
PubMed-ID: 16772301 | Reference-DOI: 10.1074/JBC.M601777200

Molecule 1 - AGGLUTININ-1 A CHAIN
	Chains	:	A
	EC Number	:	3.2.2.22
	Fragment	:	RESIDUES 21-280
	Organism Common	:	INDIAN LICORICE
	Organism Scientific	:	ABRUS PRECATORIUS
	Organism Taxid	:	3816

Molecule 2 - AGGLUTININ-1 B CHAIN
	Chains	:	B
	Fragment	:	RESIDUES 281-547
	Organism Common	:	INDIAN LICORICE
	Organism Scientific	:	ABRUS PRECATORIUS
	Organism Taxid	:	3816

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP B:98 , ASN B:100	BINDING SITE FOR RESIDUE NAG B 501
2	AC2	SOFTWARE	ASN A:215 , THR B:15 , LEU B:48 , LEU B:53 , ASN B:140	BINDING SITE FOR RESIDUE NAG B 601
3	AC3	SOFTWARE	ASN A:215 , VAL A:227 , ASN B:140	BINDING SITE FOR RESIDUE NAG A 701

Asymmetric Unit

No.	Residues
1	A:246	-	B:8
2	B:25	-	B:44
3	B:68	-	B:85
4	B:156	-	B:169
5	B:195	-	B:212

Asymmetric Unit

No.	Residues
1	Thr A:70	-	Asn A:71
2	Asn A:71	-	Ala A:72
3	Thr B:138	-	Gly B:139

(no "SAP(SNP)/Variant" information available for 2Q3N)

Asymmetric 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.	AGGL_ABRPR	178-194	1	A:158-174
2	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	AGGL_ABRPR	292-419 422-546	2	B:12-139 B:142-266

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIGA_RICIN	PS00275	Shiga/ricin ribosomal inactivating toxins active site signature.	AGGL_ABRPR	178-194	2	A:158-174
2	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	AGGL_ABRPR	292-419 422-546	4	B:12-139 B:142-266

Biological Unit 2 (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.	AGGL_ABRPR	178-194	1	A:158-174
2	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	AGGL_ABRPR	292-419 422-546	2	B:12-139 B:142-266

(no "Exon" information available for 2Q3N)

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 AGGL_ABRPR | Q9M6E9 from UniProtKB/Swiss-Prot  Length:547

    Alignment length:247
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       
           AGGL_ABRPR    22 DPIKFTTGSATPASYNQFIDALRERLTGGLIYGIPVLRDPSTVEKPNQYVTVELSYSDTVSIQLGIDLTNAYVVAYRAGSESFFFRNAPASASTYLFTGTQQYSLPFDGNYDDLEKWAHQSRQRISLGLEALRQGIKFLRSGASDDEEIARTLIVIIQMVAEAARFRYVSKLVVISLSNRAAFQPDPSMLSLENTWEPLSRAVQHTVQDTFPQNVTLINVRQERVVVSSLSHPSVSALALMLFVCNP 268
               SCOP domains d2q3na1 A:2-248 Agglutinin-1 chain A                                                                                                                                                                                                                    SCOP domains
               CATH domains 2q3nA01 A:2-167 Ricin (A subunit), domain 1                                                                                                                           2q3nA02 A:168-248 Ricin (A Subunit), domain 2                                     CATH domains
               Pfam domains ---RIP-2q3nA01 A:5-207                                                                                                                                                                                        ----------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhhhhh.eee..eee.......hhhh.eeeeeee.....eeeeeee.....eeeeee..eeee....hhhhhhh.....eeee.....hhhhhhhhhh........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh........eeee.....eeee.....hhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      -------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q3n A   2 DPIKFTTGSATPASYNQFIDALRERLTGGLIYGIPVLRDPSTVEKPNQYVTVELSYSDTVSIQLGIDLTNAYVVAYRAGSESFFFRNAPASASTYLFTGTQQYSLPFDGNYDDLEKWAHQSRQRISLGLEALRQGIKFLRSGASDDEEIARTLIVIIQMVAEAARFRYVSKLVVISLSNRAAFQPDPSMLSLENTWEPLSRAVQHTVQDTFPQNVTLINVRQERVVVSSLSHPSVSALALMLFVCNP 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain B from PDB  Type:PROTEIN  Length:261
 aligned with AGGL_ABRPR | Q9M6E9 from UniProtKB/Swiss-Prot  Length:547

    Alignment length:261
                                   296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546 
           AGGL_ABRPR   287 ICSSHYEPTVRIGGRDGLCVDVSDNAYNNGNPIILWKCKDQLEVNQLWTLKSDKTIRSKGKCLTTYGYAPGNYVMIYDCSSAVAEATYWDIWDNGTIINPKSGLVLSAESSSMGGTLTVQKNDYRMRQGWRTGNDTSPFVTSIAGFFKLCMEAHGNSMWLDVCDITKEEQQWAVYPDGSIRPVQNTNNCLTCEEHKQGATIVMMGCSNAWASQRWVFKSDGTIYNLYDDMVMDVKSSDPSLKQIILWPYTGNANQMWATLF 547
               SCOP domains d2q3nb2 B:7-140 Agglutinin-1 chain B                                                                                                  d2q3nb1 B:141-267 Agglutinin-1 chain B                                                                                          SCOP domains
               CATH domains 2q3nB01 B:7-143  [code=2.80.10.50, no name defined]                                                                                      2q3nB02 B:144-267  [code=2.80.10.50, no name defined]                                                                        CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2q3nB01 B:142-263                                                                                          ---- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2q3nB02 B:142-263                                                                                          ---- Pfam domains (2)
         Sec.struct. author ........ee.eehhhhheeee.hhh....eeeeee......hhhhheee.....eee..eeeee........eeee.....hhhhhh.ee.....eee....eeeee........eeee....hhhhh.ee......eeeeee....eeeeee..eeeeee.........eee.....eee.....eeeee........eeeee....hhhhh.ee.....eee....eeee...........eee....hhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----RICIN_B_LECTIN  PDB: B:12-139 UniProt: 292-419                                                                                  --RICIN_B_LECTIN  PDB: B:142-266 UniProt: 422-546                                                                              - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q3n B   7 ICSSHYEPTVRIGGRDGLCVDVSDNAYNNGNPIILWKCKDQLEVNQLWTLKSDKTIRSKGKCLTTYGYAPGNYVMIYDCSSAVAEATYWDIWDNGTIINPKSGLVLSAESSSMGGTLTVQKNDYRMRQGWRTGNDTSPFVTSIAGFFKLCMEAHGNSMWLDVCDITKEEQQWAVYPDGSIRPVQNTNNCLTCEEHKQGATIVMMGCSNAWASQRWVFKSDGTIYNLYDDMVMDVKSSDPSLKQIILWPYTGNANQMWATLF 267
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266

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: All beta proteins (24004)

Fold: beta-Trefoil (385)

Superfamily: Ricin B-like lectins (91)

Family: Ricin B-like (65)

Protein domain: Agglutinin-1 chain B (2)

Abrus precatorius [TaxId: 3816] (2)

1a	d2q3nb1	B:141-267
1b	d2q3nb2	B:7-140

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: Agglutinin-1 chain A (1)

Abrus precatorius [TaxId: 3816] (1)

d2q3na1

A:2-248

Asymmetric Unit(hide GO term definitions)

Chain A,B (AGGL_ABRPR | Q9M6E9)

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: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:0007157	heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules	The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
	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:0044533	positive regulation of apoptotic process in other organism	Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death by apoptosis in a second organism.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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		Asn A:71 - Ala A:72	[ RasMol ]
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		Thr B:138 - Gly B:139	[ RasMol ]

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	2q3n
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(no "Related Entries Specified in the PDB File" available for 2Q3N)

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