1WS4 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF JACALIN- ME-ALPHA-MANNOSE COMPLEX: PROMISCUITY VS SPECIFICITY

Authors :   A. A. Jeyaprakash, G. Jayashree, S. K. Mahanta, K. Sekar, A. Surolia, M. Vijayan

Date :   31 Oct 04 (Deposition) - 29 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B,C,D,E,F,G,H

Keywords :   Beta-Prism-I Fold, Post Translational Proteolysis, Lectin, Galactose-Specific, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. A. Jeyaprakash, G. Jayashree, S. K. Mahanta, C. P. Swaminathan, K. Sekar, A. Surolia, M. Vijayan
Structural Basis For The Energetics Of Jacalin-Sugar Interactions: Promiscuity Versus Specificity
J. Mol. Biol. V. 347 181 2005
PubMed-ID: 15733927 | Reference-DOI: 10.1016/J.JMB.2005.01.015
(for further references see the PDB file header)

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

Molecule 2 - AGGLUTININ BETA-3 CHAIN
	Chains	:	B, D, F, H
	Organ	:	SEEDS
	Organism Scientific	:	ARTOCARPUS INTEGER
	Organism Taxid	:	3490
	Synonym	:	JACALIN BETA-3 CHAIN

Molecule 3 - AGGLUTININ ALPHA CHAIN
	Chains	:	C, E
	Organ	:	SEEDS
	Organism Scientific	:	ARTOCARPUS INTEGER
	Organism Taxid	:	3490
	Synonym	:	JACALIN ALPHA CHAIN

		1	2	3	4	5	6	7	8
Asymmetric/Biological Unit	:	A	B	C	D	E	F	G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	AMG	1	Ligand/Ion	ALPHA-METHYL-D-GALACTOSIDE
2	GYP	3	Ligand/Ion	METHYL-ALPHA-D-GLUCOPYRANOSIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:1 , TYR A:78 , GLY A:121 , TYR A:122 , TRP A:123 , ASP A:125 , HOH A:378 , LYS F:18	BINDING SITE FOR RESIDUE GYP A 501
2	AC2	SOFTWARE	GLY C:1 , TYR C:78 , GLY C:121 , TYR C:122 , TRP C:123 , ASP C:125	BINDING SITE FOR RESIDUE GYP C 502
3	AC3	SOFTWARE	GLY E:1 , TYR E:78 , GLY E:121 , TYR E:122 , TRP E:123 , ASP E:125	BINDING SITE FOR RESIDUE AMG E 503
4	AC4	SOFTWARE	GLY G:1 , TYR G:78 , GLY G:121 , TYR G:122 , TRP G:123 , ASP G:125 , HOH G:449	BINDING SITE FOR RESIDUE GYP G 504

(no "SS Bond" information available for 1WS4)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:60	-	Pro A:61
2	Gly A:94	-	Pro A:95
3	Gly B:13	-	Pro B:14
4	Phe C:60	-	Pro C:61
5	Gly C:94	-	Pro C:95
6	Gly D:13	-	Pro D:14
7	Phe E:60	-	Pro E:61
8	Gly E:94	-	Pro E:95
9	Gly F:13	-	Pro F:14
10	Phe G:60	-	Pro G:61
11	Gly G:94	-	Pro G:95
12	Gly H:13	-	Pro H:14

Asymmetric/Biological Unit (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/C/E/G	V	31	I
02	UniProt	VAR_LECA_ARTIN_002 *	L	34	G	LECA_ARTIN	---	---	A/C/E/G	L	34	G
03	UniProt	VAR_LECA_ARTIN_003 *	K	45	L	LECA_ARTIN	---	---	A/C/E/G	V	45	L
04	UniProt	VAR_LECA_ARTIN_004 *	K	45	T	LECA_ARTIN	---	---	A/C/E/G	V	45	T
05	UniProt	VAR_LECA_ARTIN_005 *	M	66	D	LECA_ARTIN	---	---	A/C/E/G	M	66	D
06	UniProt	VAR_LECA_ARTIN_006 *	M	66	V	LECA_ARTIN	---	---	A/C/E/G	M	66	V
07	UniProt	VAR_LECA_ARTIN_007 *	E	67	M	LECA_ARTIN	---	---	A/C/E/G	E	67	M
08	UniProt	VAR_LECA_ARTIN_008 *	T	72	I	LECA_ARTIN	---	---	A/C/E/G	T	72	I
09	UniProt	VAR_LECA_ARTIN_009 *	N	74	K	LECA_ARTIN	---	---	A/C/E/G	N	74	K
10	UniProt	VAR_LECA_ARTIN_010 *	T	102	D	LECA_ARTIN	---	---	A/C/E/G	T	102	D
11	UniProt	VAR_LECA_ARTIN_011 *	I	113	V	LECA_ARTIN	---	---	A/C/E/G	I	113	V
12	UniProt	VAR_LECA_ARTIN_012 *	L	131	N	LECA_ARTIN	---	---	A/C/E/G	L	131	N
	* ID not provided by source

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

Asymmetric/Biological Unit (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 C:1-133 E:1-133 G:1-133

(no "Exon" information available for 1WS4)

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: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 ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1ws4A00 A:1-133  [code=2.100.10.30, no name defined]                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeee...........eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeeeeee.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
                 1ws4 A   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHVSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 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 ---------------- 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
                 1ws4 B   3 QSGISQTVIVGPWGAK  18
                                    12

Chain C 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 ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1ws4C00 C:1-133  [code=2.100.10.30, no name defined]                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeee...........eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
             SAPs(SNPs) (1) ------------------------------I--G-------------------------------DM----I-K---------------------------D----------V-----------------N-- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------V------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE JACALIN_LECTIN  PDB: C:1-133 UniProt: 1-133                                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ws4 C   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain D 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 ---------------- 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
                 1ws4 D   3 QSGISQTVIVGPWGAK  18
                                    12

Chain E 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 ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1ws4E00 E:1-133  [code=2.100.10.30, no name defined]                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeee...........eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
             SAPs(SNPs) (1) ------------------------------I--G-------------------------------DM----I-K---------------------------D----------V-----------------N-- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------V------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE JACALIN_LECTIN  PDB: E:1-133 UniProt: 1-133                                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ws4 E   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain F from PDB  Type:PROTEIN  Length:18
 aligned with LECB3_ARTIN | P18673 from UniProtKB/Swiss-Prot  Length:20

    Alignment length:18
                                    12        
          LECB3_ARTIN     3 QSGISQTVIVGPWGAKVS  20
               SCOP domains ------------------ 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
                 1ws4 F   3 QSGISQTVIVGPWGAKSA  20
                                    12

Chain G 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 ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1ws4G00 G:1-133  [code=2.100.10.30, no name defined]                                                                                  CATH domains
           Pfam domains (1) Jacalin-1ws4G01 G:1-133                                                                                                               Pfam domains (1)
           Pfam domains (2) Jacalin-1ws4G02 G:1-133                                                                                                               Pfam domains (2)
           Pfam domains (3) Jacalin-1ws4G03 G:1-133                                                                                                               Pfam domains (3)
           Pfam domains (4) Jacalin-1ws4G04 G:1-133                                                                                                               Pfam domains (4)
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeee...........eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeeeeee.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: G:1-133 UniProt: 1-133                                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ws4 G   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHVSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain H 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 ---------------- 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
                 1ws4 H   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 '\|'

(no "SCOP Domain" information available for 1WS4)

Asymmetric/Biological 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. (13)

1a	1ws4A00	A:1-133
1b	1ws4C00	C:1-133
1c	1ws4E00	E:1-133
1d	1ws4G00	G:1-133

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Jacalin (35)

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

1a	Jacalin-1ws4G01	G:1-133
1b	Jacalin-1ws4G02	G:1-133
1c	Jacalin-1ws4G03	G:1-133
1d	Jacalin-1ws4G04	G:1-133

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C,E,G (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,D,F,H (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:94 - Pro A:95	[ RasMol ]
		Gly B:13 - Pro B:14	[ RasMol ]
		Gly C:94 - Pro C:95	[ RasMol ]
		Gly D:13 - Pro D:14	[ RasMol ]
		Gly E:94 - Pro E:95	[ RasMol ]
		Gly F:13 - Pro F:14	[ RasMol ]
		Gly G:94 - Pro G:95	[ RasMol ]
		Gly H:13 - Pro H:14	[ RasMol ]
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1jac	A NOVEL MODE OF CARBOHYDRATE RECOGNITION IN JACALIN, A MORACEAE PLANT LECTIN WITH A BETA-PRISM
1m26	CRYSTAL STRUCTURE OF JACALIN-T-ANTIGEN COMPLEX
1ugw	CRYSTAL STRUCTURE OF JACALIN-GAL COMPLEX
1ugx	ME-ALPHA-T-ANTIGEN (GAL- BETA(1-3)-GALNAC-ALPHA-O-ME) COMPLEX
1uh1	CRYSTAL STRUCTURE OF JACALIN- GALNAC-BETA(1-3)-GAL-ALPHA-O- ME COMPLEX
1ws5	JACALIN-ME-ALPHA-MANNOSE COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (12, 48)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 4)

Pfam Domains (1, 4)

Gene Ontology (4, 8)

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