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(-) Description

Title :  AGGLUTININ FROM ABRUS PRECATORIUS
 
Authors :  J. Cheng, T. H. Lu, C. L. Liu, J. Y. Lin
Date :  22 Aug 08  (Deposition) - 25 Aug 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Keywords :  Ribosome-Inactivating Protein, Immunotoxin, Agglutinin Abrin, Glycoprotein, Hydrolase, Lectin, Plant Defense, Protein Synthesis Inhibitor, Pyrrolidone Carboxylic Acid, Toxin, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Cheng, T. H. Lu, C. L. Liu, J. Y. Lin
A Biophysical Elucidation For Less Toxicity Of Agglutinin Than Abrin-A From The Seeds Of Abrus Precatorius In Consequence Of Crystal Structure
J. Biomed. Sci. V. 17 34 2010
PubMed-ID: 20433687  |  Reference-DOI: 10.1186/1423-0127-17-34
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AGGLUTININ-1 CHAIN A
    ChainsA, C
    EC Number3.2.2.22
    Organism CommonINDIAN LICORICE
    Organism ScientificABRUS PRECATORIUS
    Organism Taxid3816
    SynonymAGGLUTININ I, AAG-A
 
Molecule 2 - AGGLUTININ-1 CHAIN B
    ChainsB, D
    Organism CommonINDIAN LICORICE
    Organism ScientificABRUS PRECATORIUS
    Organism Taxid3816
    SynonymAGGLUTININ I, AAG-B

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)ABCD
Biological Unit 2 (1x)AB  
Biological Unit 3 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2NDG-1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP B:98 , ASP B:99 , ASN B:100 , TYR B:130 , HOH B:309BINDING SITE FOR RESIDUE NDG B 268
2AC2SOFTWAREASN A:215 , THR B:15 , LEU B:48 , ASN B:140 , HOH B:299 , HOH B:310 , HOH B:314BINDING SITE FOR RESIDUE NAG B 269
3AC3SOFTWAREASN C:215 , THR D:15 , VAL D:16 , LEU D:48 , ASN D:140 , HOH D:289BINDING SITE FOR RESIDUE NAG D 268

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:246 -B:8
2B:25 -B:44
3B:68 -B:85
4B:156 -B:169
5B:195 -B:212
6C:246 -D:8
7D:25 -D:44
8D:68 -D:85
9D:156 -D:169
10D:195 -D:212

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZR1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZR1)

(-) PROSITE Motifs  (2, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.AGGL_ABRPR178-194
 
  2A:158-174
C:158-174
2RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.AGGL_ABRPR292-419
 
422-546
 
  4B:12-139
D:12-139
B:142-266
D:142-266
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.AGGL_ABRPR178-194
 
  2A:158-174
C:158-174
2RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.AGGL_ABRPR292-419
 
422-546
 
  4B:12-139
D:12-139
B:142-266
D:142-266
Biological Unit 2 (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.AGGL_ABRPR178-194
 
  1A:158-174
-
2RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.AGGL_ABRPR292-419
 
422-546
 
  2B:12-139
-
B:142-266
-
Biological Unit 3 (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHIGA_RICINPS00275 Shiga/ricin ribosomal inactivating toxins active site signature.AGGL_ABRPR178-194
 
  1-
C:158-174
2RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.AGGL_ABRPR292-419
 
422-546
 
  2-
D:12-139
-
D:142-266

(-) Exons   (0, 0)

(no "Exon" information available for 2ZR1)

(-) Sequences/Alignments

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:250
 aligned with AGGL_ABRPR | Q9M6E9 from UniProtKB/Swiss-Prot  Length:547

    Alignment length:250
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
           AGGL_ABRPR    21 QDPIKFTTGSATPASYNQFIDALRERLTGGLIYGIPVLRDPSTVEKPNQYVTVELSYSDTVSIQLGIDLTNAYVVAYRAGSESFFFRNAPASASTYLFTGTQQYSLPFDGNYDDLEKWAHQSRQRISLGLEALRQGIKFLRSGASDDEEIARTLIVIIQMVAEAARFRYVSKLVVISLSNRAAFQPDPSMLSLENTWEPLSRAVQHTVQDTFPQNVTLINVRQERVVVSSLSHPSVSALALMLFVCNPLN 270
               SCOP domains d2zr1a_ A: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains 2zr1A01 A:1-167 Ricin (A subunit), domain 1                                                                                                                            2zr1A02 A:168-250 Ricin (A Subunit), domain 2                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhhhhhhhhhhhhhhhhhheeeee..eeee.hhhhhhhhh.eeeeeeeee..eeeeeeee.....eeeeee..eeee....hhhhhhhh....eeee.....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee..hhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zr1 A   1 QDPIKFTTGSATPASYNQFIDALRERLTGGLIYGIPVLRDPSTVEKPNQYVTVELSYSDTVSIQLGIDLTNAYVVAYRAGSESFFFRNAPASASTYLFTGTQQYSLPFDGNYDDLEKWAHQSRQRISLGLEALRQGIKFLRSGASDDEEIARTLIVIIQMVAEAARFRYVSKLVVISLSNRAAFQPDPSMLSLENTWEPLSRAVQHTVQDTFPQNVTLINVRQERVVVSSLSHPSVSALALMLFVCNPLN 250
                                    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

Chain B from PDB  Type:PROTEIN  Length:263
 aligned with AGGL_ABRPR | Q9M6E9 from UniProtKB/Swiss-Prot  Length:547

    Alignment length:263
                                   294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544   
           AGGL_ABRPR   285 SKICSSHYEPTVRIGGRDGLCVDVSDNAYNNGNPIILWKCKDQLEVNQLWTLKSDKTIRSKGKCLTTYGYAPGNYVMIYDCSSAVAEATYWDIWDNGTIINPKSGLVLSAESSSMGGTLTVQKNDYRMRQGWRTGNDTSPFVTSIAGFFKLCMEAHGNSMWLDVCDITKEEQQWAVYPDGSIRPVQNTNNCLTCEEHKQGATIVMMGCSNAWASQRWVFKSDGTIYNLYDDMVMDVKSSDPSLKQIILWPYTGNANQMWATLF 547
               SCOP domains d2zr1b1 B:5-140 Agglutinin-1 chain B                                                                                                    d2zr1b2 B:141-267 Agglutinin-1 chain B                                                                                          SCOP domains
               CATH domains 2zr1B01 B:5-143  [code=2.80.10.50, no name defined]                                                                                        2zr1B02 B:144-267  [code=2.80.10.50, no name defined]                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee.eehhhhheeee.hhh......eeee......hhhhheee.....eee..eeeee........eeee.....hhhhhh.ee.....eee....eeee..........eee....hhhhh.ee......eeeeee....eeeeee..eeeeee....hhhh.eee.....eee.....eeeee........eeeee.hhhhhhhh.ee.....eee....eeeee.hhhhhhh.eeee....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
                 2zr1 B   5 SKICSSHYEPTVRIGGRDGLCVDVSDNAYNNGNPIILWKCKDQLEVNQLWTLKSDKTIRSKGKCLTTYGYAPGNYVMIYDCSSAVAEATYWDIWDNGTIINPKSGLVLSAESSSMGGTLTVQKNDYRMRQGWRTGNDTSPFVTSIAGFFKLCMEAHGNSMWLDVCDITKEEQQWAVYPDGSIRPVQNTNNCLTCEEHKQGATIVMMGCSNAWASQRWVFKSDGTIYNLYDDMVMDVKSSDPSLKQIILWPYTGNANQMWATLF 267
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264   

Chain C from PDB  Type:PROTEIN  Length:250
 aligned with AGGL_ABRPR | Q9M6E9 from UniProtKB/Swiss-Prot  Length:547

    Alignment length:250
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
           AGGL_ABRPR    21 QDPIKFTTGSATPASYNQFIDALRERLTGGLIYGIPVLRDPSTVEKPNQYVTVELSYSDTVSIQLGIDLTNAYVVAYRAGSESFFFRNAPASASTYLFTGTQQYSLPFDGNYDDLEKWAHQSRQRISLGLEALRQGIKFLRSGASDDEEIARTLIVIIQMVAEAARFRYVSKLVVISLSNRAAFQPDPSMLSLENTWEPLSRAVQHTVQDTFPQNVTLINVRQERVVVSSLSHPSVSALALMLFVCNPLN 270
               SCOP domains d2zr1c_ C: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains 2zr1C01 C:1-167 Ricin (A subunit), domain 1                                                                                                                            2zr1C02 C:168-250 Ricin (A Subunit), domain 2                                       CATH domains
           Pfam domains (1) ----RIP-2zr1C01 C:5-207                                                                                                                                                                                        ------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----RIP-2zr1C02 C:5-207                                                                                                                                                                                        ------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eee.hhhhhhhhhhhhhhhhhhheeeee..eeee.hhhhh.....eeeeeee.....eeeeeee.....eeeeee..eeeee...hhhhhhh.....eeeee....hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee..hhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------SHIGA_RICIN      ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zr1 C   1 QDPIKFTTGSATPASYNQFIDALRERLTGGLIYGIPVLRDPSTVEKPNQYVTVELSYSDTVSIQLGIDLTNAYVVAYRAGSESFFFRNAPASASTYLFTGTQQYSLPFDGNYDDLEKWAHQSRQRISLGLEALRQGIKFLRSGASDDEEIARTLIVIIQMVAEAARFRYVSKLVVISLSNRAAFQPDPSMLSLENTWEPLSRAVQHTVQDTFPQNVTLINVRQERVVVSSLSHPSVSALALMLFVCNPLN 250
                                    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

Chain D from PDB  Type:PROTEIN  Length:263
 aligned with AGGL_ABRPR | Q9M6E9 from UniProtKB/Swiss-Prot  Length:547

    Alignment length:263
                                   294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544   
           AGGL_ABRPR   285 SKICSSHYEPTVRIGGRDGLCVDVSDNAYNNGNPIILWKCKDQLEVNQLWTLKSDKTIRSKGKCLTTYGYAPGNYVMIYDCSSAVAEATYWDIWDNGTIINPKSGLVLSAESSSMGGTLTVQKNDYRMRQGWRTGNDTSPFVTSIAGFFKLCMEAHGNSMWLDVCDITKEEQQWAVYPDGSIRPVQNTNNCLTCEEHKQGATIVMMGCSNAWASQRWVFKSDGTIYNLYDDMVMDVKSSDPSLKQIILWPYTGNANQMWATLF 547
               SCOP domains d2zr1d1 D:5-140 Agglutinin-1 chain B                                                                                                    d2zr1d2 D:141-267 Agglutinin-1 chain B                                                                                          SCOP domains
               CATH domains 2zr1D01 D:5-143  [code=2.80.10.50, no name defined]                                                                                        2zr1D02 D:144-267  [code=2.80.10.50, no name defined]                                                                        CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2zr1D01 D:142-263                                                                                          ---- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2zr1D02 D:142-263                                                                                          ---- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2zr1D03 D:142-263                                                                                          ---- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2zr1D04 D:142-263                                                                                          ---- Pfam domains (4)
         Sec.struct. author ..........ee.eehhhhheeee.hhh......eeee......hhhhheeee...eeee..eeeee......eeeeee.....hhhhhh.ee.....ee......eee.......ee.eee....hhhhh.ee......eeeeee....eeeeee..eeeeee....hhh.eeee.....eee.....eeeee........eeeee.hhh......eee...eeee....eeeee.hhhhhhh.eeee....hhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------RICIN_B_LECTIN  PDB: D:12-139 UniProt: 292-419                                                                                  --RICIN_B_LECTIN  PDB: D:142-266 UniProt: 422-546                                                                              - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zr1 D   5 SKICSSHYEPTVRIGGRDGLCVDVSDNAYNNGNPIILWKCKDQLEVNQLWTLKSDKTIRSKGKCLTTYGYAPGNYVMIYDCSSAVAEATYWDIWDNGTIINPKSGLVLSAESSSMGGTLTVQKNDYRMRQGWRTGNDTSPFVTSIAGFFKLCMEAHGNSMWLDVCDITKEEQQWAVYPDGSIRPVQNTNNCLTCEEHKQGATIVMMGCSNAWASQRWVFKSDGTIYNLYDDMVMDVKSSDPSLKQIILWPYTGNANQMWATLF 267
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264   

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 6)

Asymmetric Unit

(-) CATH Domains  (3, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 6)

Asymmetric Unit
(-)
Clan: Trefoil (131)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AGGL_ABRPR | Q9M6E92q3n

(-) Related Entries Specified in the PDB File

1abr THE SAME PROTEIN CRYSTALLIZED IN DIFFERENT CRYSTAL FORM
2q3n THE SAME PROTEIN CRYSTALLIZED IN DIFFERENT CRYSTAL FORM