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Asym./Biol. Unit (Jmol Viewer)

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

Title :   PTEROCARPUS ANGOLENSIS LECTIN (PAL) IN COMPLEX WITH THE GLCNAC(BETA1-2)MAN DISACCHARIDE

Authors :   L. Buts, A. Garcia-Pino, A. Imberty, N. Amiot, G. -J. Boons, W. Versees, S. Beeckmans, L. Wyns, R. Loris

Date :   19 Aug 05 (Deposition) - 01 Aug 06 (Release) - 29 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

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

Reference :   L. Buts, A. Garcia-Pino, A. Imberty, N. Amiot, G. J. Boons, S. Beeckmans, W. Versees, L. Wyns, R. Loris
Structural Basis For The Recognition Of Complex-Type Biantennary Oligosaccharides By Pterocarpus Angolensis Lectin.
Febs J. V. 273 2407 2006
PubMed-ID: 16704415 | Reference-DOI: 10.1111/J.1742-4658.2006.05248.X

Molecule 1 - LECTIN
	Chains	:	A, B
	Organism Scientific	:	PTEROCARPUS ANGOLENSIS
	Organism Taxid	:	182271
	Synonym	:	PAL
	Tissue	:	SEED

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 8)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
3	MN	2	Ligand/Ion	MANGANESE (II) ION
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:45 , GLY A:102 , GLY A:104 , LEU A:107 , GLY A:220 , MAN A:254 , HOH A:310 , HOH A:313	BINDING SITE FOR RESIDUE NAG A 253
2	AC2	SOFTWARE	ASP A:86 , GLY A:105 , GLY A:106 , PHE A:132 , ASN A:138 , GLY A:220 , GLU A:221 , GLN A:222 , NAG A:253	BINDING SITE FOR RESIDUE MAN A 254
3	AC3	SOFTWARE	SER B:45 , GLY B:102 , GLY B:104 , GLY B:220 , MAN B:254 , HOH B:328	BINDING SITE FOR RESIDUE NAG B 253
4	AC4	SOFTWARE	ALA B:85 , ASP B:86 , GLY B:106 , PHE B:132 , ASN B:138 , GLY B:220 , GLU B:221 , GLN B:222 , NAG B:253	BINDING SITE FOR RESIDUE MAN B 254
5	AC5	SOFTWARE	GLU A:128 , ASP A:130 , ASP A:141 , HIS A:146 , HOH A:266 , HOH A:267	BINDING SITE FOR RESIDUE MN A 261
6	AC6	SOFTWARE	GLU B:128 , ASP B:130 , ASP B:141 , HIS B:146 , HOH B:267 , HOH B:268	BINDING SITE FOR RESIDUE MN B 262
7	AC7	SOFTWARE	ASP A:130 , PHE A:132 , ASN A:138 , ASP A:141 , HOH A:264 , HOH A:265	BINDING SITE FOR RESIDUE CA A 263
8	AC8	SOFTWARE	ASP B:130 , PHE B:132 , ASN B:138 , ASP B:141 , HOH B:265 , HOH B:266	BINDING SITE FOR RESIDUE CA B 264

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

Asymmetric/Biological Unit

No.	Residues
1	Ala A:85	-	Asp A:86
2	Ala B:85	-	Asp B:86

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

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

(no "Exon" information available for 2ARB)

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:240
 aligned with Q8GSD2_PTEAG | Q8GSD2 from UniProtKB/TrEMBL  Length:260

    Alignment length:240
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248
         Q8GSD2_PTEAG     9 QDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAPGTAQNTSANQVIAVEFDTFYAQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLYT 248
               SCOP domains d2arba_ A: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains 2arbA00 A:1-240  [code=2.60.120.200, no name defined]                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.........eeeee..eee..eee.............eeeeeee...ee.ee....eeeeeeeeeeeeee........eeeeeee..........hhhhh...hhhhh.hhhhh..eeeeee...............eeeeee......eeee........eeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeeee.....eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2arb A   1 QDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAPGTAQNTSANQVIAVEFDTFYAQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLYT 240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain B from PDB  Type:PROTEIN  Length:240
 aligned with Q8GSD2_PTEAG | Q8GSD2 from UniProtKB/TrEMBL  Length:260

    Alignment length:240
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248
         Q8GSD2_PTEAG     9 QDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAPGTAQNTSANQVIAVEFDTFYAQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLYT 248
               SCOP domains d2arbb_ B: automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains 2arbB00 B:1-240  [code=2.60.120.200, no name defined]                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.........eeeee..eee..eee.............eeeeeee...ee.ee....eeeeeeeeeeeeee........eeeeeee..........hhhhh...hhhhh........eeeeee...............eeeeee......eeee........eeeeeeee....eeeeeee.....eeeeeee.hhhhh...eeeeeeeeee.....eeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2arb B   1 QDSLSFGFPTFPSDQKNLIFQGDAQIKNNAVQLTKTDSNGNPVASTVGRILFSAQVHLWEKSSSRVANFQSQFSFSLKSPLSNGADGIAFFIAPPDTTIPSGSGGGLLGLFAPGTAQNTSANQVIAVEFDTFYAQDSNTWDPNYPHIGIDVNSIRSVKTVKWDRRDGQSLNVLVTFNPSTRNLDVVATYSDGTRYEVSYEVDVRSVLPEWVRVGFSAASGEQYQTHTLESWSFTSTLLYT 240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

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)

Bloodwood tree (Pterocarpus angolensis) [TaxId: 182271] (21)

1a	d2arba_	A:
1b	d2arbb_	B:

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)

Pterocarpus angolensis. Organism_taxid: 182271. (14)

1a	2arbA00	A:1-240
1b	2arbB00	B:1-240

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q8GSD2_PTEAG | Q8GSD2)

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
	Complete Structure
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	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MAN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:85 - Asp A:86	[ RasMol ]
		Ala B:85 - Asp B:86	[ RasMol ]

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1q8o	RELATED COMPLEX
1s1a	LIGAND-FREE PROTEIN
2ar6	RELATED COMPLEX
2are

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (1, 2)

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