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Title :   CRYSTAL STRUCTURE OF A LECTIN FROM CANAVALIA GLADIATA SEEDS (CGL) IN COMPLEX WITH MAN1-4MAN-OME

Authors :   F. B. M. B. Moreno, G. A. Bezerra, T. M. Oliveira, E. P. Souza, B. A. M. Rocha, G. B. Benevides, P. Delatorre, B. S. Cavada, W. F. De Azevedo Jr.

Date :   07 Mar 07 (Deposition) - 23 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.98

Chains :   Asym. Unit : A,B,C,D,O^#,P^#,Q^#,R^#
Biol. Unit 1: A,B,C,D  (1x)
( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Keywords :   Dimannoside, Man1-4Man-Ome, Canavalia Gladiata Lectin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. A. Bezerra, T. M. Oliveira, F. B. Moreno, E. P. De Souza, B. A. Da Rocha, R. G. Benevides, P. Delatorre, W. F. De Azevedo, B. S. Cavada
Structural Analysis Of Canavalia Maritima And Canavalia Gladiata Lectins Complexed With Different Dimannosides: New Insights Into The Understanding Of The Structure-Biological Activity Relationship In Legume Lectins.
J. Struct. Biol. V. 160 168 2007
PubMed-ID: 17881248 | Reference-DOI: 10.1016/J.JSB.2007.07.012
(for further references see the PDB file header)

Molecule 1 - CANAVALIA GLADIATA LECTIN
	Chains	:	A, B, C, D
	Organism Common	:	SWORD BEAN
	Organism Scientific	:	CANAVALIA GLADIATA
	Organism Taxid	:	3824
	Other Details	:	PROTEIN FROM PLANT SEEDS

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	O^#	P^#	Q^#	R^#
Biological Unit 1 (1x)	:	A	B	C	D

( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 16)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
3	MMA	4	Ligand/Ion	O1-METHYL-MANNOSE
4	MN	4	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MAN	-1	Ligand/Ion	ALPHA-D-MANNOSE
3	MMA	-1	Ligand/Ion	O1-METHYL-MANNOSE
4	MN	-1	Ligand/Ion	MANGANESE (II) ION

(no "Site" information available for 2P2K)

(no "SS Bond" information available for 2P2K)

Asymmetric Unit

No.	Residues
1	Gly A:149	-	Thr A:150
2	Ser A:204	-	His A:205
3	Ala A:207	-	Asp A:208
4	Ser B:117	-	Asn B:118
5	Thr B:150	-	Asp B:151
6	Ala B:207	-	Asp B:208
7	Gly C:149	-	Thr C:150
8	Ala C:207	-	Asp C:208
9	Ser D:117	-	Asn D:118
10	Gly D:149	-	Thr D:150
11	Thr D:150	-	Asp D:151
12	Ala D:207	-	Asp D:208
13	Leu D:229	-	Leu D:230

(no "SAP(SNP)/Variant" information available for 2P2K)

(no "PROSITE Motif" information available for 2P2K)

(no "Exon" information available for 2P2K)

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:234
 aligned with CONA_CANGL | P14894 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:234
                                                          1         12         13          25                         26   31  32 35                36                                                                                                                
                                     -         -         -|       10 |       -  |     20    |    -         -         - |    |  -|  |     -         - |      44        54        64        74        84        94       104       114       124       134       144    
           CONA_CANGL     - ------------------------------MAISKKSSLFLP----------IFTFITMFLMVVN--------------------------KVSSST---HETN-----------------ALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 148
               SCOP domains d2p2ka_ A: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains 2p2kA00 A:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee....eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2p2k A   1 ADTIVAVELDTYPNTDIGDPNYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110       123       133       143       153       163       173       183       193       203       213       223       233    
                                                                                                                                                119|                                                                                                                  
                                                                                                                                                 123

Chain B from PDB  Type:PROTEIN  Length:234
 aligned with CONA_CANGL | P14894 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:234
                                                          1         12         13          25                         26   31                   32                                                                                                                    
                                     -         -         -|       10 |       -  |     20    |    -         -         - |    |  -         -       |34        44        54        64        74        84        94       104       114       124       134       144    
           CONA_CANGL     - ------------------------------MAISKKSSLFLP----------IFTFITMFLMVVN--------------------------KVSSST--------------------HETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 148
               SCOP domains d2p2kb_ B: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains 2p2kB00 B:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee...eeeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2p2k B   1 ADTIVAVELDTYPNTDIGDPNYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110       123       133       143       153       163       173       183       193       203       213       223       233    
                                                                                                                                               118|                                                                                                                   
                                                                                                                                                122

Chain C from PDB  Type:PROTEIN  Length:234
 aligned with CONA_CANGL | P14894 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:234
                                                          1         12         13          25                         26   31  32 35                36                                                                                                                
                                     -         -         -|       10 |       -  |     20    |    -         -         - |    |  -|  |     -         - |      44        54        64        74        84        94       104       114       124       134       144    
           CONA_CANGL     - ------------------------------MAISKKSSLFLP----------IFTFITMFLMVVN--------------------------KVSSST---HETN-----------------ALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 148
               SCOP domains d2p2kc_ C: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains 2p2kC00 C:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee...eeeeeeee.........eeeee..ee.....ee...ee...ee....eeeeee...ee.......eeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2p2k C   1 ADTIVAVELDTYPNTDIGDPNYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNSTNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110       123       133       143       153       163       173       183       193       203       213       223       233    
                                                                                                                                                119|                                                                                                                  
                                                                                                                                                 123

Chain D from PDB  Type:PROTEIN  Length:234
 aligned with CONA_CANGL | P14894 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:234
                                                          1         12         13          25                         26   31                   32                                                                                                                    
                                     -         -         -|       10 |       -  |     20    |    -         -         - |    |  -         -       |34        44        54        64        74        84        94       104       114       124       134       144    
           CONA_CANGL     - ------------------------------MAISKKSSLFLP----------IFTFITMFLMVVN--------------------------KVSSST--------------------HETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 148
               SCOP domains d2p2kd_ D: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains 2p2kD00 D:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                      CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------Lectin_legB-2p2kD01 D:124-237                                                                                      Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------Lectin_legB-2p2kD02 D:124-237                                                                                      Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------Lectin_legB-2p2kD03 D:124-237                                                                                      Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------Lectin_legB-2p2kD04 D:124-237                                                                                      Pfam domains (4)
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee...eeeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2p2k D   1 ADTIVAVELDTYPNTDIGDPNYPHIGIDIKSVRSKKTAKWNMQNGKVGTAHIIYNSVGKRLSAVVSYPNGDSATVSYDVDLDNVLPEWVRVGLSASTGLYKETNTILSWSFTSKLKSNETNALHFMFNQFSKDQKDLILQGDATTGTDGNLELTRVSSNGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSHPADGIAFFISNIDSSIPSGSTGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110       123       133       143       153       163       173       183       193       203       213       223       233    
                                                                                                                                               118|                                                                                                                   
                                                                                                                                                122

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: Legume lectins (238)

Protein domain: automated matches (63)

Canavalia gladiata [TaxId: 3824] (5)

1a	d2p2ka_	A:
1b	d2p2kb_	B:
1c	d2p2kc_	C:
1d	d2p2kd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.200, no name defined] (421)

Sword bean (Canavalia gladiata) (5)

1a	2p2kA00	A:1-237
1b	2p2kB00	B:1-237
1c	2p2kC00	C:1-237
1d	2p2kD00	D:1-237

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Concanavalin (293)

Family: Lectin_legB (93)

Canavalia gladiata (Sword bean) (Dolichos gladiatus) (3)

1a	Lectin_legB-2p2kD01	D:124-237
1b	Lectin_legB-2p2kD02	D:124-237
1c	Lectin_legB-2p2kD03	D:124-237
1d	Lectin_legB-2p2kD04	D:124-237

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CONA_CANGL | P14894)

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:0005537	mannose binding	Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0048029	monosaccharide binding	Interacting selectively and non-covalently with any monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
biological process
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0051781	positive regulation of cell division	Any process that activates or increases the frequency, rate or extent of cell division.
	GO:0045840	positive regulation of mitotic nuclear division	Any process that activates or increases the frequency, rate or extent of mitosis.
	GO:0050688	regulation of defense response to virus	Any process that modulates the frequency, rate or extent of the antiviral response of a cell or organism.
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 Unit
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	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MAN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MMA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 2p2k)

	Cis Peptide Bonds
		Ala A:207 - Asp A:208	[ RasMol ]
		Ala B:207 - Asp B:208	[ RasMol ]
		Ala C:207 - Asp C:208	[ RasMol ]
		Ala D:207 - Asp D:208	[ RasMol ]
		Gly A:149 - Thr A:150	[ RasMol ]
		Gly C:149 - Thr C:150	[ RasMol ]
		Gly D:149 - Thr D:150	[ RasMol ]
		Leu D:229 - Leu D:230	[ RasMol ]
		Ser A:204 - His A:205	[ RasMol ]
		Ser B:117 - Asn B:118	[ RasMol ]
		Ser D:117 - Asn D:118	[ RasMol ]
		Thr B:150 - Asp B:151	[ RasMol ]
		Thr D:150 - Asp D:151	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	2p2k
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		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
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	CONA_CANGL \| P14894
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	CONA_CANGL \| P14894	:	1wuv 2d7f 2ef6 2ovu

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (13, 13)

Sequence-Structure Mapping

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