4AKB - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF GALACTOSE BINDING LECTIN FROM CHAMPEDAK (CGB) WITH GALACTOSE

Authors :   M. Gabrielsen, P. S. Abdul-Rahman, S. Othman, O. H. Hashim, R. J. Cogdel

Date :   22 Feb 12 (Deposition) - 27 Feb 13 (Release) - 18 Jun 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

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

Reference :   M. Gabrielsen, P. S. Abdul-Rahman, S. Othman, O. H. Hashim, R. J. Cogdell
Structures And Binding Specificity Of Galactose- And Mannose-Binding Lectins From Champedak: Differences From Jackfruit Lectins
Acta Crystallogr. , Sect. F V. 70 709 2014
PubMed-ID: 24915077 | Reference-DOI: 10.1107/S2053230X14008966

Molecule 1 - AGGLUTININ ALPHA CHAIN
	Chains	:	A, C, E, G
	Organism Scientific	:	ARTOCARPUS INTEGER
	Organism Taxid	:	3490
	Synonym	:	JACALIN ALPHA CHAIN, CHAMPEDAK GALACTOSE BINDING LECTIN ALPHA CHAIN

Molecule 2 - AGGLUTININ BETA-4 CHAIN
	Chains	:	B, D, F, H
	Organism Scientific	:	ARTOCARPUS INTEGER
	Organism Taxid	:	3490
	Synonym	:	CHAMPEDAK GALACTOSE BINDING LECTIN BETA 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	GAL	3	Ligand/Ion	BETA-D-GALACTOSE
2	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:47 , VAL A:80 , GLY A:121 , TYR A:122 , TRP A:123 , ASP A:125	BINDING SITE FOR RESIDUE P6G A1134
2	AC2	SOFTWARE	GLY C:1 , PHE C:47 , TYR C:78 , GLY C:121 , TYR C:122 , TRP C:123 , ASP C:125	BINDING SITE FOR RESIDUE GAL C1134
3	AC3	SOFTWARE	GLY E:1 , PHE E:47 , TYR E:78 , GLY E:121 , TYR E:122 , TRP E:123 , ASP E:125 , HOH E:2001 , HOH E:2079	BINDING SITE FOR RESIDUE GAL E1134
4	AC4	SOFTWARE	GLY G:1 , PHE G:47 , TYR G:78 , GLY G:121 , TYR G:122 , TRP G:123 , ASP G:125	BINDING SITE FOR RESIDUE GAL G1134

(no "SS Bond" information available for 4AKB)

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	K	45	L
04	UniProt	VAR_LECA_ARTIN_004 *	K	45	T	LECA_ARTIN	---	---	A/C/E/G	K	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	K	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 4AKB)

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 ------------------------------------------------------------------------------------------------------------------------------------- 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
                 4akb A   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGENHKSFITGFTPVKISLDFPSEYIMEVSGYTGKVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFSLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:15
 aligned with LECB4_ARTIN | Q9S8T0 from UniProtKB/Swiss-Prot  Length:20

    Alignment length:15
                                    13     
          LECB4_ARTIN     4 SGISQTVIVGPWGAQ  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
                 4akb B   4 SGISQTVIVGPWGAQ  18
                                    13

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 ------------------------------------------------------------------------------------------------------------------------------------- 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: C:1-133 UniProt: 1-133                                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4akb C   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGENHKSFITGFTPVKISLDFPSEYIMEVSGYTGKVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFSLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain D from PDB  Type:PROTEIN  Length:16
 aligned with LECB4_ARTIN | Q9S8T0 from UniProtKB/Swiss-Prot  Length:20

    Alignment length:16
                                    12      
          LECB4_ARTIN     3 QSGISQTVIVGPWGAQ  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
                 4akb D   3 QSGISQTVIVGPWGAQ  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 ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeee...........eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeee.....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: E:1-133 UniProt: 1-133                                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4akb E   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGENHKSFITGFTPVKISLDFPSEYIMEVSGYTGKVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFSLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain F from PDB  Type:PROTEIN  Length:15
 aligned with LECB4_ARTIN | Q9S8T0 from UniProtKB/Swiss-Prot  Length:20

    Alignment length:15
                                    12     
          LECB4_ARTIN     3 QSGISQTVIVGPWGA  17
               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
                 4akb F   3 QSGISQTVIVGPWGA  17
                                    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 ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeee...........eeeeee.........eeeeeeeee..eeeeeeeeee....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
                 4akb G   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGENHKSFITGFTPVKISLDFPSEYIMEVSGYTGKVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFSLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain H from PDB  Type:PROTEIN  Length:16
 aligned with LECB4_ARTIN | Q9S8T0 from UniProtKB/Swiss-Prot  Length:20

    Alignment length:16
                                    12      
          LECB4_ARTIN     3 QSGISQTVIVGPWGAQ  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
                 4akb H   3 QSGISQTVIVGPWGAQ  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 4AKB)

(no "CATH Domain" information available for 4AKB)

(no "Pfam Domain" information available for 4AKB)

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 (LECB4_ARTIN | Q9S8T0)

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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	Ligands, Modified Residues, Ions
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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 ]
		Phe A:60 - Pro A:61	[ RasMol ]
		Phe C:60 - Pro C:61	[ RasMol ]
		Phe E:60 - Pro E:61	[ RasMol ]
		Phe G:60 - Pro G:61	[ RasMol ]

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4ak4	HIGH RESOLUTION STRUCTURE OF GALACTOSE BINDING LECTIN FROM CHAMPEDAK (CGB)
4akc	STRUCTURE OF GALACTOSE BINDING LECTIN FROM CHAMPEDAK ( CGB) WITH GAL(BETA)1,3-GALNAC
4akd	HIGH RESOLUTION STRUCTURE OF MANNOSE BINDING LECTIN FROM CHAMPEDAK (CMB)

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

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (4, 8)

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