5AV7 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CALSEPA LECTIN IN COMPLEX WITH BISECTED GLYCAN

Authors :   M. Nagae, Y. Yamaguchi

Date :   12 Jun 15 (Deposition) - 27 Apr 16 (Release) - 27 Apr 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

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

Reference :   M. Nagae, M. Kanagawa, K. Morita-Matsumoto, S. Hanashima, Y. Kizuka, N. Taniguchi, Y. Yamaguchi
Atomic Visualization Of A Flipped-Back Conformation Of Bisected Glycans Bound To Specific Lectins
Sci Rep V. 6 22973 2016
PubMed-ID: 26971576 | Reference-DOI: 10.1038/SREP22973

Molecule 1 - LECTIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HEDGE BINDWEED
	Organism Scientific	:	CALYSTEGIA SEPIUM
	Organism Taxid	:	47519

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
2	MMA	2	Ligand/Ion	O1-METHYL-MANNOSE
3	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
2	MMA	1	Ligand/Ion	O1-METHYL-MANNOSE
3	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
2	MMA	1	Ligand/Ion	O1-METHYL-MANNOSE
3	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:16 , GLY A:17 , ASN A:18 , GLY A:64 , ASP A:95 , ASN A:96 , GLY A:140 , TYR A:141 , TYR A:142 , ASP A:144 , HOH A:309 , HOH A:313 , GLY B:16 , GLY B:17 , ASN B:18 , GLY B:64 , LEU B:94 , ASP B:95 , ASN B:96 , GLY B:140 , TYR B:141 , TYR B:142 , ASP B:144	binding site for Poly-Saccharide residues MMA A 201 through NAG A 206
2	AC2	SOFTWARE	GLY A:16 , GLY A:17 , ASN A:18 , GLY A:64 , ASP A:95 , ASN A:96 , GLY A:140 , TYR A:141 , TYR A:142 , ASP A:144 , HOH A:309 , HOH A:313 , GLY B:16 , GLY B:17 , ASN B:18 , GLY B:64 , LEU B:94 , ASP B:95 , ASN B:96 , GLY B:140 , TYR B:141 , TYR B:142 , ASP B:144 , GLY C:16 , GLY C:17 , ASN C:18 , GLY C:64 , ASP C:95 , ASN C:96 , GLY C:140 , TYR C:141 , TYR C:142 , ASP C:144 , HOH C:317 , HOH C:321 , HOH C:325 , HOH C:335 , HOH C:340 , GLY D:17 , ASN D:18 , GLY D:64 , LEU D:94 , ASP D:95 , ASN D:96 , GLY D:140 , TYR D:141 , TYR D:142 , ASP D:144 , HOH D:209	binding site for Poly-Saccharide residues MMA C 201 through NAG C 206

(no "SS Bond" information available for 5AV7)

Asymmetric Unit

No.	Residues
1	Gly A:10	-	Pro A:11
2	Gly A:112	-	Pro A:113
3	Gly B:10	-	Pro B:11
4	Gly B:112	-	Pro B:113
5	Gly C:10	-	Pro C:11
6	Gly C:112	-	Pro C:113
7	Gly D:10	-	Pro D:11
8	Gly D:112	-	Pro D:113

(no "SAP(SNP)/Variant" information available for 5AV7)

(no "PROSITE Motif" information available for 5AV7)

(no "Exon" information available for 5AV7)

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:141
                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee....eeeee.....eeeeeeeee....eeeeeeeee...eeeee......eeeeeeee......eeeeeeeeee....eeeeeeeeee...eeeeee....eeee...eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5av7 A   3 VPMDTISGPWGNNGGNFWSFRPVNKINQIVISYGGGGNNPIALTFSSTKDTITVGGGGPDSITGTEMVNIGTDEYLTGISGTFGIYLDNNVLRSITFTTNLKAHGPYGQKVGTPFSSANEIVGFLGRSGYYVDAIGTYNRH 152
                                    12        22        32        42       |57        67        77        87        97       107       117       131       141       151 
                                                                          50|                                                                  125|                      
                                                                           56                                                                   130

Chain B from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee....eeeee.......eeeeeee....eeeeeeeeee.....eeeeeee........eeeeee......eeeeeeeeee....eeeeeeeeee...eeeeee....eeee.....eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5av7 B   3 VPMDTISGPWGNNGGNFWSFRPVNKINQIVISYGGGGNNPIALTFSSTKADGSKDTITVGGGGPDSITGTEMVNIGTDEYLTGISGTFGIYLDNNVLRSITFTTNLKAHGPYGQKVGTPFSSANVNEIVGFLGRSGYYVDAIGTYNRH 152
                                    12        22        32        42        52        62        72        82        92       102       112       122    || 134       144        
                                                                                                                                                      127|                      
                                                                                                                                                       130

Chain C from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee....eeeee.......eeeeeee....eeeeeeeeee.....eeeeeee......eeeeeeee......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeee.....eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5av7 C   3 VPMDTISGPWGNNGGNFWSFRPVNKINQIVISYGGGGNNPIALTFSSTKADGSKDTITVGGGGPDSITGTEMVNIGTDEYLTGISGTFGIYLDNNVLRSITFTTNLKAHGPYGQKVGTPFSSANVNEIVGFLGRSGYYVDAIGTYNRH 152
                                    12        22        32        42        52        62        72        82        92       102       112       122    || 134       144        
                                                                                                                                                      127|                      
                                                                                                                                                       130

Chain D from PDB  Type:PROTEIN  Length:147
                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee....eeeee.....eeeeeeeee....eeeeeeeee.......eeeee......eeeeeeee......eeeeeeeeee....eeeeeeeeee...eeeeee....eeee.....eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5av7 D   3 VPMDTISGPWGNNGGNFWSFRPVNKINQIVISYGGGGNNPIALTFSSTKAGSKDTITVGGGGPDSITGTEMVNIGTDEYLTGISGTFGIYLDNNVLRSITFTTNLKAHGPYGQKVGTPFSSANVNEIVGFLGRSGYYVDAIGTYNRH 152
                                    12        22        32        42        52|       63        73        83        93       103       113       123   ||  135       145       
                                                                            52|                                                                      127|                      
                                                                             54                                                                       130

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 '\|'

(no "SCOP Domain" information available for 5AV7)

(no "CATH Domain" information available for 5AV7)

(no "Pfam Domain" information available for 5AV7)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 5AV7)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		MAN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MMA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:10 - Pro A:11	[ RasMol ]
		Gly A:112 - Pro A:113	[ RasMol ]
		Gly B:10 - Pro B:11	[ RasMol ]
		Gly B:112 - Pro B:113	[ RasMol ]
		Gly C:10 - Pro C:11	[ RasMol ]
		Gly C:112 - Pro C:113	[ RasMol ]
		Gly D:10 - Pro D:11	[ RasMol ]
		Gly D:112 - Pro D:113	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	P93114_CALSE \| P93114
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	P93114_CALSE \| P93114	:	1ouw

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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