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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF AN ANTIFLAMATORY LEGUME LECTIN FROM CYMBOSEMA ROSEUM SEEDS

Authors :   B. A. M. Rocha, P. Delatorre, E. S. Marinho, R. G. Benevides, T. R. Moura, L. A. G. Souza, K. S. Nascimento, A. H. Sampaio, B. S. Cavada

Date :   20 Mar 09 (Deposition) - 07 Apr 10 (Release) - 16 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,C,E,G

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

Reference :   B. A. Rocha, P. Delatorre, T. M. Oliveira, R. G. Benevides, A. F. Pires, A. A. Sousa, L. A. Souza, S. A. Ana Maria, H. Debray, W. F. De Azevedo, A. H. Sampaio, B. S. Cavada
Structural Basis For Both Pro- And Anti-Inflammatory Response Induced By Mannose-Specific Legume Lectin From Cymbosema Roseum
Biochimie 2011
PubMed-ID: 21277932 | Reference-DOI: 10.1016/J.BIOCHI.2011.01.006

Molecule 1 - CYMBOSEMA ROSEUM MANNOSE-SPECIFIC LECTIN
	Chains	:	A, C, E, G
	Organism Scientific	:	CYMBOSEMA ROSEUM
	Organism Taxid	:	202239
	Other Details	:	SEEDS

		1	2	3	4
Asymmetric/Biological Unit	:	A	C	E	G

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	ABA	2	Ligand/Ion	ALPHA-AMINOBUTYRIC ACID
2	CA	4	Ligand/Ion	CALCIUM ION
3	MN	4	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:289 , HOH A:494	BINDING SITE FOR RESIDUE MN A 238
02	AC2	SOFTWARE	ASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:259 , HOH A:503	BINDING SITE FOR RESIDUE CA A 239
03	AC3	SOFTWARE	GLU C:8 , ASP C:10 , ASP C:19 , HIS C:24 , HOH C:537 , HOH C:556	BINDING SITE FOR RESIDUE MN C 238
04	AC4	SOFTWARE	ASP C:10 , TYR C:12 , ASN C:14 , ASP C:19 , HOH C:256 , HOH C:536	BINDING SITE FOR RESIDUE CA C 239
05	AC5	SOFTWARE	GLU E:8 , ASP E:10 , ASP E:19 , HIS E:24 , HOH E:545 , HOH E:557	BINDING SITE FOR RESIDUE MN E 238
06	AC6	SOFTWARE	ASP E:10 , TYR E:12 , ASN E:14 , ASP E:19 , HOH E:269 , HOH E:304	BINDING SITE FOR RESIDUE CA E 239
07	AC7	SOFTWARE	TRP E:88 , ASN E:124 , ALA E:125 , HIS E:180 , HOH E:540 , HOH E:553 , HOH E:558 , PHE G:128 , SER G:129 , PHE G:130 , ASP G:139 , HOH G:319	BINDING SITE FOR RESIDUE ABA E 240
08	AC8	SOFTWARE	GLU G:8 , ASP G:10 , ASP G:19 , HIS G:24 , HOH G:546 , HOH G:547	BINDING SITE FOR RESIDUE MN G 238
09	AC9	SOFTWARE	ASP G:10 , TYR G:12 , ASN G:14 , ASP G:19 , HOH G:323 , HOH G:538	BINDING SITE FOR RESIDUE CA G 239
10	BC1	SOFTWARE	PHE E:130 , ASP E:139 , SER G:113 , LYS G:114 , ALA G:125 , LEU G:126 , VAL G:179 , HIS G:180 , HOH G:254 , HOH G:302	BINDING SITE FOR RESIDUE ABA G 240

(no "SS Bond" information available for 3A0K)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:207	-	Asp A:208
2	Ala C:207	-	Asp C:208
3	Ala E:207	-	Asp E:208
4	Ala G:207	-	Asp G:208

(no "SAP(SNP)/Variant" information available for 3A0K)

(no "PROSITE Motif" information available for 3A0K)

(no "Exon" information available for 3A0K)

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:232
 aligned with D5MNX4_CYMRO | D5MNX4 from UniProtKB/TrEMBL  Length:237

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
         D5MNX4_CYMRO     1 ADTIVAVELDSYPNTDIGDPSYPHIGIDIKSIRSKSTARWNMQTGKVGTAHISYNSVAKRLTAVVSYSGSSSTTVSYDVDLTNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANALHFSFNQFTQNPKDLILQGDATTDSDGNLELTKVSSSGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSEPADGITFFIANTDTSIPSGSSGRLLGLFPDAN 237
               SCOP domains d3a0ka_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 3a0kA00 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....eeeeeeee.....eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee.-----.eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a0k A   1 ADTIVAVELDSYPNTDIGDPSYPHIGIDIKSIRSKSTARWNMQTGKVGTAHISYNSVAKRLTAVVSYSGSSSTTVSYDVDLTNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKT-----ANALHFSFNQFTQNPKDLILQGDATTDSDGNLELTKVSSSGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSEPADGITFFIANTDTSIPSGSSGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110      |  -  |    130       140       150       160       170       180       190       200       210       220       230       
                                                                                                                                              117   123

Chain C from PDB  Type:PROTEIN  Length:232
 aligned with D5MNX4_CYMRO | D5MNX4 from UniProtKB/TrEMBL  Length:237

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
         D5MNX4_CYMRO     1 ADTIVAVELDSYPNTDIGDPSYPHIGIDIKSIRSKSTARWNMQTGKVGTAHISYNSVAKRLTAVVSYSGSSSTTVSYDVDLTNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANALHFSFNQFTQNPKDLILQGDATTDSDGNLELTKVSSSGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSEPADGITFFIANTDTSIPSGSSGRLLGLFPDAN 237
               SCOP domains d3a0kc_ C: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 3a0kC00 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....eeeeeeee.....eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee.-----.eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a0k C   1 ADTIVAVELDSYPNTDIGDPSYPHIGIDIKSIRSKSTARWNMQTGKVGTAHISYNSVAKRLTAVVSYSGSSSTTVSYDVDLTNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKT-----ANALHFSFNQFTQNPKDLILQGDATTDSDGNLELTKVSSSGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSEPADGITFFIANTDTSIPSGSSGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110      |  -  |    130       140       150       160       170       180       190       200       210       220       230       
                                                                                                                                              117   123

Chain E from PDB  Type:PROTEIN  Length:237
 aligned with D5MNX4_CYMRO | D5MNX4 from UniProtKB/TrEMBL  Length:237

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
         D5MNX4_CYMRO     1 ADTIVAVELDSYPNTDIGDPSYPHIGIDIKSIRSKSTARWNMQTGKVGTAHISYNSVAKRLTAVVSYSGSSSTTVSYDVDLTNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANALHFSFNQFTQNPKDLILQGDATTDSDGNLELTKVSSSGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSEPADGITFFIANTDTSIPSGSSGRLLGLFPDAN 237
               SCOP domains d3a0ke_ E: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 3a0kE00 E: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
                 3a0k E   1 ADTIVAVELDSYPNTDIGDPSYPHIGIDIKSIRSKSTARWNMQTGKVGTAHISYNSVAKRLTAVVSYSGSSSTTVSYDVDLTNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANALHFSFNQFTQNPKDLILQGDATTDSDGNLELTKVSSSGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSEPADGITFFIANTDTSIPSGSSGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain G from PDB  Type:PROTEIN  Length:237
 aligned with D5MNX4_CYMRO | D5MNX4 from UniProtKB/TrEMBL  Length:237

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
         D5MNX4_CYMRO     1 ADTIVAVELDSYPNTDIGDPSYPHIGIDIKSIRSKSTARWNMQTGKVGTAHISYNSVAKRLTAVVSYSGSSSTTVSYDVDLTNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANALHFSFNQFTQNPKDLILQGDATTDSDGNLELTKVSSSGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSEPADGITFFIANTDTSIPSGSSGRLLGLFPDAN 237
               SCOP domains d3a0kg_ G: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 3a0kG00 G: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......eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeeee......eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a0k G   1 ADTIVAVELDSYPNTDIGDPSYPHIGIDIKSIRSKSTARWNMQTGKVGTAHISYNSVAKRLTAVVSYSGSSSTTVSYDVDLTNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANALHFSFNQFTQNPKDLILQGDATTDSDGNLELTKVSSSGSPQGSSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDSEPADGITFFIANTDTSIPSGSSGRLLGLFPDAN 237
                                    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)

Cymbosema roseum [TaxId: 202239] (1)

1a	d3a0ka_	A:
1b	d3a0kc_	C:
1c	d3a0ke_	E:
1d	d3a0kg_	G:

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)

Cymbosema roseum. Organism_taxid: 202239. (1)

1a	3a0kA00	A:1-237
1b	3a0kC00	C:1-237
1c	3a0kE00	E:1-237
1d	3a0kG00	G:1-237

(no "Pfam Domain" information available for 3A0K)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C,E,G (D5MNX4_CYMRO | D5MNX4)

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:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		ABA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Ala A:207 - Asp A:208	[ RasMol ]
		Ala C:207 - Asp C:208	[ RasMol ]
		Ala E:207 - Asp E:208	[ RasMol ]
		Ala G:207 - Asp G:208	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3A0K)

Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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