2D3P - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRATYLIA FLORIBUNDA SEED LECTIN CRYSTALLIZED AT BASIC PH

Authors :   F. G. Del Sol, B. S. Cavada, J. J. Calvete

Date :   30 Sep 05 (Deposition) - 10 Nov 05 (Release) - 12 Jan 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

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

Reference :   F. G. Del Sol, B. S. Cavada, J. J. Calvete
Crystal Structures Of Cratylia Floribunda Seed Lectin At Acidic And Basic Phs. Insights Into The Structural Basis Of The Ph-Dependent Dimer-Tetramer Transition.
J. Struct. Biol. V. 158 1 2007
PubMed-ID: 17251039 | Reference-DOI: 10.1016/J.JSB.2006.08.014
(for further references see the PDB file header)

Molecule 1 - LECTIN ALPHA CHAIN
	Chains	:	A, B, C, D
	Organism Scientific	:	CRATYLIA ARGENTEA
	Organism Taxid	:	83131

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	MN	4	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:10 , TYR A:12 , ASN A:14 , ASP A:19	BINDING SITE FOR RESIDUE CA A 237
2	AC2	SOFTWARE	GLU A:8 , ASP A:10 , ASP A:19 , HIS A:24	BINDING SITE FOR RESIDUE MN A 238
3	AC3	SOFTWARE	ASP B:10 , TYR B:12 , ASN B:14 , ASP B:19	BINDING SITE FOR RESIDUE CA B 239
4	AC4	SOFTWARE	GLU B:8 , ASP B:10 , ASP B:19 , HIS B:24	BINDING SITE FOR RESIDUE MN B 240
5	AC5	SOFTWARE	ASP C:10 , TYR C:12 , ASN C:14 , ASP C:19 , HOH C:244	BINDING SITE FOR RESIDUE CA C 241
6	AC6	SOFTWARE	GLU C:8 , ASP C:10 , ASP C:19 , HIS C:24	BINDING SITE FOR RESIDUE MN C 242
7	AC7	SOFTWARE	ASP D:10 , TYR D:12 , ASN D:14 , ASP D:19	BINDING SITE FOR RESIDUE CA D 243
8	AC8	SOFTWARE	GLU D:8 , ASP D:10 , ASP D:19 , HIS D:24	BINDING SITE FOR RESIDUE MN D 244

(no "SS Bond" information available for 2D3P)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:206	-	Asp A:207
2	Ala B:206	-	Asp B:207
3	Ala C:206	-	Asp C:207
4	Ala D:206	-	Asp D:207

(no "SAP(SNP)/Variant" information available for 2D3P)

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LECTIN_LEGUME_BETA	PS00307	Legume lectins beta-chain signature.	LECA_CRAAG	5-11	4	A:5-11 B:5-11 C:5-11 D:5-11
2	LECTIN_LEGUME_ALPHA	PS00308	Legume lectins alpha-chain signature.	LECA_CRAAG	85-94	4	A:85-94 B:85-94 C:85-94 D:85-94

(no "Exon" information available for 2D3P)

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:236
 aligned with LECA_CRAAG | P81517 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
           LECA_CRAAG     1 ADTIVAVELDTYPNTDIGDPNYQHIGINIKSIRSKATTRWNVQDGKVGTAHISYNSVAKRLSAIVSYPGGSSATVSYDVDLNNILPEWVRVGLSASTGLYKETNTILSWSFTSKLKTNSTADAQSLHFTFNQFSQNPKDLILQGDASTDSDGNLQLTRVSNGSPQSNSVGRALYYAPVHVWDKSAVVASFDATFTFLIKSTDSDIADGIAWFIANTDSSIPHGSGGRLLGLFPDAN 236
               SCOP domains d2d3pa_ A: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains 2d3pA00 A:1-236  [code=2.60.120.200, no name defined]                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeeee...eeeeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee.......eeeeeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee.......eeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d3p A   1 ADTIVAVELDTYPNTDIGDPNYQHIGINIKSIRSKATTRWNVQDGKVGTAHISYNSVAKRLSAIVSYPGGSSATVSYDVDLNNILPEWVRVGLSASTGLYKETNTILSWSFTSKLKTNSTADAQSLHFTFNQFSQNPKDLILQGDASTDSDGNLQLTRVSNGSPQSNSVGRALYYAPVHVWDKSAVVASFDATFTFLIKSTDSDIADGIAFFIANTDSSIPHGSGGRLLGLFPDAN 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:236
 aligned with LECA_CRAAG | P81517 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
           LECA_CRAAG     1 ADTIVAVELDTYPNTDIGDPNYQHIGINIKSIRSKATTRWNVQDGKVGTAHISYNSVAKRLSAIVSYPGGSSATVSYDVDLNNILPEWVRVGLSASTGLYKETNTILSWSFTSKLKTNSTADAQSLHFTFNQFSQNPKDLILQGDASTDSDGNLQLTRVSNGSPQSNSVGRALYYAPVHVWDKSAVVASFDATFTFLIKSTDSDIADGIAWFIANTDSSIPHGSGGRLLGLFPDAN 236
               SCOP domains d2d3pb_ B: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains 2d3pB00 B:1-236  [code=2.60.120.200, no name defined]                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee.......eeeeeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee.......eeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d3p B   1 ADTIVAVELDTYPNTDIGDPNYQHIGINIKSIRSKATTRWNVQDGKVGTAHISYNSVAKRLSAIVSYPGGSSATVSYDVDLNNILPEWVRVGLSASTGLYKETNTILSWSFTSKLKTNSTADAQSLHFTFNQFSQNPKDLILQGDASTDSDGNLQLTRVSNGSPQSNSVGRALYYAPVHVWDKSAVVASFDATFTFLIKSTDSDIADGIAFFIANTDSSIPHGSGGRLLGLFPDAN 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain C from PDB  Type:PROTEIN  Length:236
 aligned with LECA_CRAAG | P81517 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
           LECA_CRAAG     1 ADTIVAVELDTYPNTDIGDPNYQHIGINIKSIRSKATTRWNVQDGKVGTAHISYNSVAKRLSAIVSYPGGSSATVSYDVDLNNILPEWVRVGLSASTGLYKETNTILSWSFTSKLKTNSTADAQSLHFTFNQFSQNPKDLILQGDASTDSDGNLQLTRVSNGSPQSNSVGRALYYAPVHVWDKSAVVASFDATFTFLIKSTDSDIADGIAWFIANTDSSIPHGSGGRLLGLFPDAN 236
               SCOP domains d2d3pc_ C: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains 2d3pC00 C:1-236  [code=2.60.120.200, no name defined]                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee.......eeeeeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee.......eeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d3p C   1 ADTIVAVELDTYPNTDIGDPNYQHIGINIKSIRSKATTRWNVQDGKVGTAHISYNSVAKRLSAIVSYPGGSSATVSYDVDLNNILPEWVRVGLSASTGLYKETNTILSWSFTSKLKTNSTADAQSLHFTFNQFSQNPKDLILQGDASTDSDGNLQLTRVSNGSPQSNSVGRALYYAPVHVWDKSAVVASFDATFTFLIKSTDSDIADGIAFFIANTDSSIPHGSGGRLLGLFPDAN 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain D from PDB  Type:PROTEIN  Length:236
 aligned with LECA_CRAAG | P81517 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
           LECA_CRAAG     1 ADTIVAVELDTYPNTDIGDPNYQHIGINIKSIRSKATTRWNVQDGKVGTAHISYNSVAKRLSAIVSYPGGSSATVSYDVDLNNILPEWVRVGLSASTGLYKETNTILSWSFTSKLKTNSTADAQSLHFTFNQFSQNPKDLILQGDASTDSDGNLQLTRVSNGSPQSNSVGRALYYAPVHVWDKSAVVASFDATFTFLIKSTDSDIADGIAWFIANTDSSIPHGSGGRLLGLFPDAN 236
               SCOP domains d2d3pd_ D: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains 2d3pD00 D:1-236  [code=2.60.120.200, no name defined]                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee.......eee.......eeeeeeeee....eeeeeeee...eeeeeeee.hhhhh.....eeeeeee........eeeeeeeeeeee.......eeeeeee.........eeeee..ee.....ee...ee..ee....eeeeee............eeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d3p D   1 ADTIVAVELDTYPNTDIGDPNYQHIGINIKSIRSKATTRWNVQDGKVGTAHISYNSVAKRLSAIVSYPGGSSATVSYDVDLNNILPEWVRVGLSASTGLYKETNTILSWSFTSKLKTNSTADAQSLHFTFNQFSQNPKDLILQGDASTDSDGNLQLTRVSNGSPQSNSVGRALYYAPVHVWDKSAVVASFDATFTFLIKSTDSDIADGIAFFIANTDSSIPHGSGGRLLGLFPDAN 236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

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)

Cratylia argentea [TaxId: 83131] (2)

1a	d2d3pa_	A:
1b	d2d3pb_	B:
1c	d2d3pc_	C:
1d	d2d3pd_	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)

Cratylia argentea. Organism_taxid: 83131 (2)

1a	2d3pA00	A:1-236
1b	2d3pB00	B:1-236
1c	2d3pC00	C:1-236
1d	2d3pD00	D:1-236

(no "Pfam Domain" information available for 2D3P)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (LECA_CRAAG | P81517)

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.
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
		Ala A:206 - Asp A:207	[ RasMol ]
		Ala B:206 - Asp B:207	[ RasMol ]
		Ala C:206 - Asp C:207	[ RasMol ]
		Ala D:206 - Asp D:207	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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Exons (0, 0)

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