1Y2X - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE TETRAGONAL FORM OF THE COMMON EDIBLE MUSHROOM (AGARICUS BISPORUS) LECTIN IN COMPLEX WITH T-ANTIGEN AND N-ACETYLGLUCOSAMINE

Authors :   M. E. Carrizo, S. Capaldi, M. Perduca, F. J. Irazoqui, G. A. Nores, H. L. M

Date :   23 Nov 04 (Deposition) - 21 Dec 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.36

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

Keywords :   Abl, Agaricus Bisporus, Lectin, Mushroom, T-Antigen, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Carrizo, S. Capaldi, M. Perduca, F. J. Irazoqui, G. A. Nores, H. L. Monaco
The Antineoplastic Lectin Of The Common Edible Mushroom (Agaricus Bisporus) Has Two Binding Sites, Each Specific Fo A Different Configuration At A Single Epimeric Hydroxyl
J. Biol. Chem. V. 280 10614 2005
PubMed-ID: 15596442 | Reference-DOI: 10.1074/JBC.M411989200
(for further references see the PDB file header)

Molecule 1 - LECTIN
	Chains	:	A, B, C, D
	Organism Scientific	:	AGARICUS BISPORUS
	Organism Taxid	:	5341

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 16)

No.	Name	Count	Type	Full Name
1	GAL	4	Ligand/Ion	BETA-D-GALACTOSE
2	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NGA	4	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
4	SER	4	Mod. Amino Acid	SERINE

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:79 , ILE A:80 , VAL A:81 , THR A:82 , ILE A:102 , ARG A:103 , TYR A:114 , VAL A:116	BINDING SITE FOR RESIDUE NAG A 144
02	AC2	SOFTWARE	ASP B:79 , ILE B:80 , VAL B:81 , THR B:82 , ILE B:102 , ARG B:103 , TYR B:114 , VAL B:116 , HOH B:1158 , ASN C:83	BINDING SITE FOR RESIDUE NAG B 1144
03	AC3	SOFTWARE	ASN B:83 , ASP C:79 , ILE C:80 , VAL C:81 , THR C:82 , ILE C:102 , ARG C:103 , TYR C:114 , VAL C:116	BINDING SITE FOR RESIDUE NAG C 2144
04	AC4	SOFTWARE	ASN A:109 , ASP D:79 , ILE D:80 , VAL D:81 , THR D:82 , ILE D:102 , ARG D:103 , TYR D:114 , VAL D:116 , HOH D:3160	BINDING SITE FOR RESIDUE NAG D 3144
05	AC5	SOFTWARE	TYR A:28 , SER A:48 , GLY A:49 , HIS A:72 , ASN A:73 , TYR A:74 , ARG A:107 , GAL A:146 , SER A:147	BINDING SITE FOR RESIDUE NGA A 145
06	AC6	SOFTWARE	TYR A:28 , ALA A:29 , SER A:48 , NGA A:145	BINDING SITE FOR RESIDUE GAL A 146
07	AC7	SOFTWARE	TYR B:28 , SER B:48 , GLY B:49 , HIS B:72 , ASN B:73 , TYR B:74 , ARG B:107 , GAL B:146 , SER B:147	BINDING SITE FOR RESIDUE NGA B 145
08	AC8	SOFTWARE	TYR B:28 , ALA B:29 , SER B:48 , NGA B:145	BINDING SITE FOR RESIDUE GAL B 146
09	AC9	SOFTWARE	TYR C:28 , SER C:48 , GLY C:49 , HIS C:72 , ASN C:73 , TYR C:74 , ARG C:107 , GAL C:146 , SER C:147 , HOH C:2148	BINDING SITE FOR RESIDUE NGA C 145
10	BC1	SOFTWARE	TYR C:28 , ALA C:29 , SER C:48 , NGA C:145	BINDING SITE FOR RESIDUE GAL C 146
11	BC2	SOFTWARE	TYR D:28 , SER D:48 , GLY D:49 , HIS D:72 , ASN D:73 , TYR D:74 , ARG D:107 , GAL D:146 , SER D:147	BINDING SITE FOR RESIDUE NGA D 145
12	BC3	SOFTWARE	TYR D:28 , ALA D:29 , SER D:48 , NGA D:145	BINDING SITE FOR RESIDUE GAL D 146
13	BC4	SOFTWARE	ASN A:73 , NGA A:145	BINDING SITE FOR RESIDUE SER A 147
14	BC5	SOFTWARE	ASN B:73 , NGA B:145	BINDING SITE FOR RESIDUE SER B 147
15	BC6	SOFTWARE	ASN C:73 , NGA C:145	BINDING SITE FOR RESIDUE SER C 147
16	BC7	SOFTWARE	ASN D:73 , NGA D:145	BINDING SITE FOR RESIDUE SER D 147

(no "SS Bond" information available for 1Y2X)

(no "Cis Peptide Bond" information available for 1Y2X)

(no "SAP(SNP)/Variant" information available for 1Y2X)

(no "PROSITE Motif" information available for 1Y2X)

(no "Exon" information available for 1Y2X)

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:142
 aligned with ABL_AGABI | Q00022 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
            ABL_AGABI     2 TYTISIRVYQTTPKGFFRPVERTNWKYANGGTWDEVRGEYVLTMGGSGTSGSLRFVSSDTDESFVATFGVHNYKRWCDIVTNLTNEQTALVINQEYYGVPIRDQARENQLTSYNVANAKGRRFAIEYTVTEGDNLKANLIIG 143
               SCOP domains d1y2xa_ A: TF antigen-binding lectin                                                                                                           SCOP domains
               CATH domains 1y2xA00 A:2-143  [code=2.60.270.20, no name defined]                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.......eeeeeee......eeeeee..eeeeee.....eeeeeeee....eeeeeeeeee..eeeeeeee......hhhhhhhhh..hhhhhhhhhh...eeeee.....eeeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y2x A   2 TYTISIRVYQTTPKGFFRPVERTNWKYANGGTWDEVRGEYVLTMGGSGTSGSLRFVSSDTDESFVATFGVHNYKRWCDIVTNLTNEQTALVINQEYYGVPIRDQARENQLTSYNVANAKGRRFAIEYTVTEGDNLKANLIIG 143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with ABL_AGABI | Q00022 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
            ABL_AGABI     2 TYTISIRVYQTTPKGFFRPVERTNWKYANGGTWDEVRGEYVLTMGGSGTSGSLRFVSSDTDESFVATFGVHNYKRWCDIVTNLTNEQTALVINQEYYGVPIRDQARENQLTSYNVANAKGRRFAIEYTVTEGDNLKANLIIG 143
               SCOP domains d1y2xb_ B: TF antigen-binding lectin                                                                                                           SCOP domains
               CATH domains 1y2xB00 B:2-143  [code=2.60.270.20, no name defined]                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.......eeeeeee.hhhh.eeeeee..eeeeee.....eeeeeeee....eeeeeeeeee..eeeeeeee......hhhhhhhhh..hhhhhhhhhh...eeeee.....eeeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y2x B   2 TYTISIRVYQTTPKGFFRPVERTNWKYANGGTWDEVRGEYVLTMGGSGTSGSLRFVSSDTDESFVATFGVHNYKRWCDIVTNLTNEQTALVINQEYYGVPIRDQARENQLTSYNVANAKGRRFAIEYTVTEGDNLKANLIIG 143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain C from PDB  Type:PROTEIN  Length:142
 aligned with ABL_AGABI | Q00022 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
            ABL_AGABI     2 TYTISIRVYQTTPKGFFRPVERTNWKYANGGTWDEVRGEYVLTMGGSGTSGSLRFVSSDTDESFVATFGVHNYKRWCDIVTNLTNEQTALVINQEYYGVPIRDQARENQLTSYNVANAKGRRFAIEYTVTEGDNLKANLIIG 143
               SCOP domains d1y2xc_ C: TF antigen-binding lectin                                                                                                           SCOP domains
               CATH domains 1y2xC00 C:2-143  [code=2.60.270.20, no name defined]                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.......eeeeeee......eeeeee..eeeeee.....eeeeeeee....eeeeeeeeee..eeeeeeee......hhhhhhhhh..hhhhhhhhhh...eeeee.....eeeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y2x C   2 TYTISIRVYQTTPKGFFRPVERTNWKYANGGTWDEVRGEYVLTMGGSGTSGSLRFVSSDTDESFVATFGVHNYKRWCDIVTNLTNEQTALVINQEYYGVPIRDQARENQLTSYNVANAKGRRFAIEYTVTEGDNLKANLIIG 143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

Chain D from PDB  Type:PROTEIN  Length:142
 aligned with ABL_AGABI | Q00022 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:142
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  
            ABL_AGABI     2 TYTISIRVYQTTPKGFFRPVERTNWKYANGGTWDEVRGEYVLTMGGSGTSGSLRFVSSDTDESFVATFGVHNYKRWCDIVTNLTNEQTALVINQEYYGVPIRDQARENQLTSYNVANAKGRRFAIEYTVTEGDNLKANLIIG 143
               SCOP domains d1y2xd_ D: TF antigen-binding lectin                                                                                                           SCOP domains
               CATH domains 1y2xD00 D:2-143  [code=2.60.270.20, no name defined]                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.......eeeeeee......eeeeee..eeeeee.....eeeeeeee....eeeeeeeeee..eeeeeeee......hhhhhhhhh..hhhhhhhhhh...eeeee.....eeeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y2x D   2 TYTISIRVYQTTPKGFFRPVERTNWKYANGGTWDEVRGEYVLTMGGSGTSGSLRFVSSDTDESFVATFGVHNYKRWCDIVTNLTNEQTALVINQEYYGVPIRDQARENQLTSYNVANAKGRRFAIEYTVTEGDNLKANLIIG 143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Cytolysin/lectin (26)

Superfamily: Cytolysin/lectin (26)

Family: Fungal fruit body lectin (17)

Protein domain: TF antigen-binding lectin (5)

Common mushroom (Agaricus bisporus) [TaxId: 5341] (5)

1a	d1y2xa_	A:
1b	d1y2xc_	C:
1c	d1y2xd_	D:
1d	d1y2xb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Mutm (Fpg) Protein; Chain: A, domain 2 (18)

Homologous Superfamily: [code=2.60.270.20, no name defined] (18)

Agaricus bisporus. Organism_taxid: 5341 (5)

1a	1y2xA00	A:2-143
1b	1y2xC00	C:2-143
1c	1y2xD00	D:2-143
1d	1y2xB00	B:2-143

(no "Pfam Domain" information available for 1Y2X)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (ABL_AGABI | Q00022)

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.

Asymmetric/Biological Unit
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	1y2x
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UniProtKB/Swiss-Prot
	ABL_AGABI \| Q00022	:	1y2t 1y2u 1y2v 1y2w

1y2t	THE SAME PROTEIN
1y2u	THE SAME PROTEIN IN COMPLEX WITH LACTO-N-BIOSE
1y2v	THE SAME PROTEIN IN COMPLEX WITH T-ANTIGEN
1y2w	THE SAME PROTEIN IN COMPLEX WITH T-ANTIGEN AND N- ACETYLGLUCOSAMINE, ORTHORHOMBIC FORM

Description

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Ligands, Modified Residues, Ions (4, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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