2EF6 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CANAVALIA GLADIATA LECTIN COMPLEXED WITH MAN1-3MAN-OME

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

Date :   21 Feb 07 (Deposition) - 30 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Canavalia Gladiata, Lectin, Seeds, Dimannosides, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. A. Bezerra, T. M. Oliveira, F. B. M. B. Moreno, E. P. De Souza, B. A. M. Da Rocha, R. G. Benevides, P. Delatorre, W. F. De Azevedo Jr. , 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 - CONCANAVALIN A
	Chains	:	A, B, C, D
	Organism Common	:	SWORD BEAN
	Organism Scientific	:	CANAVALIA GLADIATA
	Organism Taxid	:	3824
	Synonym	:	LECTIN
	Tissue	:	SEED

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 12)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	MDM	4	Ligand/Ion	METHYL-O3-(ALPHA-D-MANNOSE)-ALPHA-D-MANNOSE
3	MN	4	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:185 , GLN B:132 , TYR D:12 , ASN D:14 , GLY D:98 , LEU D:99 , TYR D:100 , ALA D:207 , ASP D:208 , GLY D:227 , ARG D:228	BINDING SITE FOR RESIDUE MDM D 1001
02	AC2	SOFTWARE	TYR A:12 , ASN A:14 , GLY A:98 , LEU A:99 , TYR A:100 , ALA A:207 , ASP A:208 , GLY A:227 , ARG A:228 , VAL B:57 , HOH B:1097 , HOH B:1111 , THR D:74 , HOH D:1069	BINDING SITE FOR RESIDUE MDM A 1002
03	AC3	SOFTWARE	GLN A:132 , SER B:185 , TYR C:12 , ASN C:14 , GLY C:98 , LEU C:99 , TYR C:100 , ALA C:207 , ASP C:208 , GLY C:227 , ARG C:228 , HOH C:1080	BINDING SITE FOR RESIDUE MDM C 1003
04	AC4	SOFTWARE	VAL A:57 , LYS A:59 , HOH A:1079 , TYR B:12 , ASN B:14 , GLY B:98 , LEU B:99 , TYR B:100 , ALA B:207 , ASP B:208 , GLY B:227 , ARG B:228 , HOH B:1117 , THR C:74 , SER C:76	BINDING SITE FOR RESIDUE MDM B 1004
05	AC5	SOFTWARE	ASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:1004 , HOH A:1037	BINDING SITE FOR RESIDUE CA A 238
06	AC6	SOFTWARE	GLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:1063 , HOH A:1118	BINDING SITE FOR RESIDUE MN A 239
07	AC7	SOFTWARE	ASP B:10 , TYR B:12 , ASN B:14 , ASP B:19 , HOH B:1013 , HOH B:1063	BINDING SITE FOR RESIDUE CA B 238
08	AC8	SOFTWARE	GLU B:8 , ASP B:10 , ASP B:19 , HIS B:24 , HOH B:1033 , HOH B:1138	BINDING SITE FOR RESIDUE MN B 239
09	AC9	SOFTWARE	ASP C:10 , TYR C:12 , ASN C:14 , ASP C:19 , HOH C:1010 , HOH C:1032	BINDING SITE FOR RESIDUE CA C 238
10	BC1	SOFTWARE	GLU C:8 , ASP C:10 , ASP C:19 , HIS C:24 , HOH C:1078 , HOH C:1079	BINDING SITE FOR RESIDUE MN C 239
11	BC2	SOFTWARE	ASP D:10 , TYR D:12 , ASN D:14 , ASP D:19 , HOH D:1015 , HOH D:1043	BINDING SITE FOR RESIDUE CA D 238
12	BC3	SOFTWARE	GLU D:8 , ASP D:10 , ASP D:19 , HIS D:24 , HOH D:1068	BINDING SITE FOR RESIDUE MN D 239

(no "SS Bond" information available for 2EF6)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:149	-	Thr A:150
2	Ala A:207	-	Asp A:208
3	Gly B:149	-	Thr B:150
4	Ala B:207	-	Asp B:208
5	Gly C:149	-	Thr C:150
6	Ala C:207	-	Asp C:208
7	Gly D:149	-	Thr D:150
8	Thr D:150	-	Asp D:151
9	Ala D:207	-	Asp D:208

(no "SAP(SNP)/Variant" information available for 2EF6)

(no "PROSITE Motif" information available for 2EF6)

(no "Exon" information available for 2EF6)

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: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 d2ef6a_ A: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains 2ef6A00 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......eeeeeeeeeeeeee....eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeeeee........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ef6 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 d2ef6b_ B: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains 2ef6B00 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....eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ef6 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 d2ef6c_ C: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains 2ef6C00 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....eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ef6 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 d2ef6d_ D: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains 2ef6D00 D: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..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ef6 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/Biological 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	d2ef6a_	A:
1b	d2ef6b_	B:
1c	d2ef6c_	C:
1d	d2ef6d_	D:

Asymmetric/Biological 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	2ef6A00	A:1-237
1b	2ef6B00	B:1-237
1c	2ef6C00	C:1-237
1d	2ef6D00	D:1-237

(no "Pfam Domain" information available for 2EF6)

Asymmetric/Biological 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/Biological Unit
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	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 B:149 - Thr B:150	[ RasMol ]
		Gly C:149 - Thr C:150	[ RasMol ]
		Gly D:149 - Thr D:150	[ RasMol ]
		Thr D:150 - Asp D:151	[ RasMol ]

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	2ef6
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	CONA_CANGL \| P14894	:	1wuv 2d7f 2ovu 2p2k

(no "Related Entries Specified in the PDB File" available for 2EF6)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 4)

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