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Description

Title :   CRYSTAL STRUCTURE OF THE COMPLEX OF JACALIN WITH MESO-TETRASULPHONATOPHENYLPORPHYRIN.

Authors :   M. Goel, P. Anuradha, K. J. Kaur, B. G. Maiya, M. J. Swamy, D. M. Salunke

Date :   03 Jul 03 (Deposition) - 03 Feb 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)

Keywords :   Lectin, Porphyrin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Goel, P. Anuradha, K. J. Kaur, B. G. Maiya, M. J. Swamy, D. M. Salunke
Porphyrin Binding To Jacalin Is Facilitated By The Inherent Plasticity Of The Carbohydrate-Binding Site: Novel Mode Of Lectin-Ligand Interaction.
Acta Crystallogr. , Sect. D V. 60 281 2004
PubMed-ID: 14747704 | Reference-DOI: 10.1107/S0907444903026684
(for further references see the PDB file header)

Compounds

Molecule 1 - AGGLUTININ ALPHA CHAIN
	Chains	:	A
	Organism Scientific	:	ARTOCARPUS INTEGER
	Organism Taxid	:	3490
	Synonym	:	JACALIN ALPHA CHAIN

Molecule 2 - AGGLUTININ BETA-3 CHAIN
	Chains	:	B
	Organism Scientific	:	ARTOCARPUS INTEGER
	Organism Taxid	:	3490
	Synonym	:	JACALIN BETA-3 CHAIN

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 2)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SFP	2	Ligand/Ion	5,10,15,20-TETRAKIS(4-SULPFONATOPHENYL)-21H,23H-PORPHINE

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	SFP	8	Ligand/Ion	5,10,15,20-TETRAKIS(4-SULPFONATOPHENYL)-21H,23H-PORPHINE

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:1 , LYS A:21 , THR A:52 , PRO A:53 , SER A:76 , TYR A:78 , TYR A:122 , SFP A:135 , HOH A:155	BINDING SITE FOR RESIDUE SFP A 134
2	AC2	SOFTWARE	ASN A:20 , LYS A:21 , GLY A:50 , PHE A:51 , THR A:52 , PRO A:53 , LYS A:91 , SFP A:134 , HOH A:160	BINDING SITE FOR RESIDUE SFP A 135

SS Bonds (0, 0)

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

Cis Peptide Bonds (3, 3)

Asymmetric Unit

No.	Residues
1	Phe A:60	-	Pro A:61
2	Gly A:94	-	Pro A:95
3	Gly B:13	-	Pro B:14

Sequence-Structure Mapping

SAPs(SNPs)/Variants (12, 12)

Asymmetric Unit (12, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_LECA_ARTIN_001 *	V	31	I	LECA_ARTIN	---	---	A	V	31	I
02	UniProt	VAR_LECA_ARTIN_002 *	L	34	G	LECA_ARTIN	---	---	A	L	34	G
03	UniProt	VAR_LECA_ARTIN_003 *	K	45	L	LECA_ARTIN	---	---	A	K	45	L
04	UniProt	VAR_LECA_ARTIN_004 *	K	45	T	LECA_ARTIN	---	---	A	K	45	T
05	UniProt	VAR_LECA_ARTIN_005 *	M	66	D	LECA_ARTIN	---	---	A	M	66	D
06	UniProt	VAR_LECA_ARTIN_006 *	M	66	V	LECA_ARTIN	---	---	A	M	66	V
07	UniProt	VAR_LECA_ARTIN_007 *	E	67	M	LECA_ARTIN	---	---	A	E	67	M
08	UniProt	VAR_LECA_ARTIN_008 *	T	72	I	LECA_ARTIN	---	---	A	T	72	I
09	UniProt	VAR_LECA_ARTIN_009 *	N	74	K	LECA_ARTIN	---	---	A	N	74	K
10	UniProt	VAR_LECA_ARTIN_010 *	T	102	D	LECA_ARTIN	---	---	A	T	102	D
11	UniProt	VAR_LECA_ARTIN_011 *	I	113	V	LECA_ARTIN	---	---	A	I	113	V
12	UniProt	VAR_LECA_ARTIN_012 *	L	131	N	LECA_ARTIN	---	---	A	L	131	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (12, 48)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_LECA_ARTIN_001 *	V	31	I	LECA_ARTIN	---	---	A	V	31	I
02	UniProt	VAR_LECA_ARTIN_002 *	L	34	G	LECA_ARTIN	---	---	A	L	34	G
03	UniProt	VAR_LECA_ARTIN_003 *	K	45	L	LECA_ARTIN	---	---	A	K	45	L
04	UniProt	VAR_LECA_ARTIN_004 *	K	45	T	LECA_ARTIN	---	---	A	K	45	T
05	UniProt	VAR_LECA_ARTIN_005 *	M	66	D	LECA_ARTIN	---	---	A	M	66	D
06	UniProt	VAR_LECA_ARTIN_006 *	M	66	V	LECA_ARTIN	---	---	A	M	66	V
07	UniProt	VAR_LECA_ARTIN_007 *	E	67	M	LECA_ARTIN	---	---	A	E	67	M
08	UniProt	VAR_LECA_ARTIN_008 *	T	72	I	LECA_ARTIN	---	---	A	T	72	I
09	UniProt	VAR_LECA_ARTIN_009 *	N	74	K	LECA_ARTIN	---	---	A	N	74	K
10	UniProt	VAR_LECA_ARTIN_010 *	T	102	D	LECA_ARTIN	---	---	A	T	102	D
11	UniProt	VAR_LECA_ARTIN_011 *	I	113	V	LECA_ARTIN	---	---	A	I	113	V
12	UniProt	VAR_LECA_ARTIN_012 *	L	131	N	LECA_ARTIN	---	---	A	L	131	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JACALIN_LECTIN	PS51752	Jacalin-type lectin domain profile.	LECA_ARTIN	1-133	1	A:1-133

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JACALIN_LECTIN	PS51752	Jacalin-type lectin domain profile.	LECA_ARTIN	1-133	4	A:1-133

Exons (0, 0)

(no "Exon" information available for 1PXD)

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:133
 aligned with LECA_ARTIN | P18670 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   
           LECA_ARTIN     1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
               SCOP domains d1pxd.1 B:,A: Jacalin                                                                                                                 SCOP domains
               CATH domains 1pxdA00 A:1-133  [code=2.100.10.30, no name defined]                                                                                  CATH domains
               Pfam domains Jacalin-1pxdA01 A:1-133                                                                                                               Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeee...........eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeee....eeeeeeeee...eeeeeeeee. Sec.struct. author
             SAPs(SNPs) (1) ------------------------------I--G----------L--------------------DM----I-K---------------------------D----------V-----------------N-- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------T--------------------V------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE JACALIN_LECTIN  PDB: A:1-133 UniProt: 1-133                                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pxd A   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:16
 aligned with LECB3_ARTIN | P18673 from UniProtKB/Swiss-Prot  Length:20

    Alignment length:16
                                    12      
          LECB3_ARTIN     3 QSGISQTVIVGPWGAK  18
               SCOP domains d1pxd.1 B:,A:    SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 1pxd B   3 QSGISQTVIVGPWGAK  18
                                    12

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 (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: beta-Prism I (50)

Superfamily: Mannose-binding lectins (42)

Family: Mannose-binding lectins (32)

Protein domain: Jacalin (12)

Jackfruit (Artocarpus heterophyllus) [TaxId: 3489] (10)

d1pxd.1

B:,A:

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Aligned Prism (39)

Topology: Vitelline Membrane Outer Layer Protein I, subunit A (39)

Homologous Superfamily: [code=2.100.10.30, no name defined] (33)

Artocarpus integer. Organism_taxid: 3490. (3)

1pxdA00

A:1-133

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Jacalin] (35)

Family: Jacalin (35)

Artocarpus integer (Jack fruit) (Artocarpus integrifolia) (15)

Jacalin-1pxdA01

A:1-133

Gene Ontology (4, 8)

Asymmetric Unit(hide GO term definitions)

Chain A (LECA_ARTIN | P18670)

molecular function
	GO:0019862	IgA binding	Interacting selectively and non-covalently with an immunoglobulin of an IgA isotype.
	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.
biological process
	GO:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

Chain B (LECB3_ARTIN | P18673)

molecular function
	GO:0019862	IgA binding	Interacting selectively and non-covalently with an immunoglobulin of an IgA isotype.
	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.
biological process
	GO:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	LECA_ARTIN \| P18670	:	1jac 1ku8 1kuj 1m26 1toq 1tp8 1ugw 1ugx 1ugy 1uh0 1uh1 1ws4 1ws5 4ak4 4akb 4akc 4r6n 4r6o 4r6p 4r6q 4r6r 5j4t 5j4x 5j50 5j51 5jm1
	LECB3_ARTIN \| P18673	:	1m26 1toq 1tp8 1ugw 1ugx 1ugy 1uh0 1uh1 1ws4 1ws5 4r6n 4r6o 4r6p 4r6q 4r6r 5j4t 5j4x 5j50 5j51 5jm1

Related Entries Specified in the PDB File

1jn2	CRYSTAL STRUCTURE OF COMPLEX OF CONA WITH MESO- TETRASULPHONATOPHENYLPORPHYRIN.