3R52 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE ANALYSIS OF A WOUND-INDUCIBLE LECTIN IPOMOELIN FROM SWEET POTATO

Authors :   K. L. Liu, W. C. Chang, S. T. Jeng, Y. S. Cheng

Date :   18 Mar 11 (Deposition) - 28 Mar 12 (Release) - 01 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Beta Prism, Carbohydrate/Sugar Binding, Carbohydrate-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. C. Chang, K. L. Liu, F. C. Hsu, S. T. Jeng, Y. S. Cheng
Ipomoelin, A Jacalin-Related Lectin With A Compact Tetrameric Association And Versatile Carbohydrate Binding Properties Regulated By Its N Terminus.
Plos One V. 7 40618 2012
PubMed-ID: 22808208 | Reference-DOI: 10.1371/JOURNAL.PONE.0040618

Molecule 1 - IPOMOELIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTZ18UH-IPO
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	BATATE
	Organism Scientific	:	IPOMOEA BATATAS
	Organism Taxid	:	4120

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 7)

No.	Name	Count	Type	Full Name
1	CD	3	Ligand/Ion	CADMIUM ION
2	GYP	4	Ligand/Ion	METHYL-ALPHA-D-GLUCOPYRANOSIDE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:21 , TYR A:97 , GLY A:141 , TRP A:142 , TYR A:143 , ASP A:145	BINDING SITE FOR RESIDUE GYP A 200
2	AC2	SOFTWARE	GLY B:21 , TYR B:97 , GLY B:141 , TRP B:142 , TYR B:143 , ASP B:145	BINDING SITE FOR RESIDUE GYP B 200
3	AC3	SOFTWARE	SER B:18 , ASN B:19 , HOH B:158 , HOH B:166 , HOH B:167	BINDING SITE FOR RESIDUE CD B 250
4	AC4	SOFTWARE	GLY C:21 , TYR C:97 , GLY C:141 , TRP C:142 , TYR C:143 , ASP C:145	BINDING SITE FOR RESIDUE GYP C 200
5	AC5	SOFTWARE	SER C:18 , ASN C:19 , HOH C:426 , HOH D:201 , HOH D:258	BINDING SITE FOR RESIDUE CD C 250
6	AC6	SOFTWARE	GLY D:21 , TYR D:97 , GLY D:141 , TRP D:142 , TYR D:143 , ASP D:145 , HOH D:343 , HOH D:346	BINDING SITE FOR RESIDUE GYP D 200
7	AC7	SOFTWARE	HOH C:171 , HOH C:175 , SER D:18 , ASN D:19 , HOH D:155 , HOH D:346	BINDING SITE FOR RESIDUE CD D 250

(no "SS Bond" information available for 3R52)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:14	-	Pro A:15
2	Asn A:57	-	Pro A:58
3	Gly A:113	-	Pro A:114
4	Gly B:14	-	Pro B:15
5	Gly B:113	-	Pro B:114
6	Gly C:14	-	Pro C:15
7	Gly C:113	-	Pro C:114
8	Gly D:14	-	Pro D:15
9	Gly D:113	-	Pro D:114

(no "SAP(SNP)/Variant" information available for 3R52)

(no "PROSITE Motif" information available for 3R52)

(no "Exon" information available for 3R52)

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:152
 aligned with P93193_IPOBA | P93193 from UniProtKB/TrEMBL  Length:154

    Alignment length:152
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152  
         P93193_IPOBA     3 LQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
               SCOP domains d3r52a_ A: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..ee.eeeeeee....eeeeee......eeeeeeee.....eeeeeeeee.....eeeee........eeeeee....eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeee....eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r52 A   3 LQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with P93193_IPOBA | P93193 from UniProtKB/TrEMBL  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
         P93193_IPOBA     2 ALQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
               SCOP domains d3r52b_ B: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..ee.eeeeeee....eeeeee......eeeeeeee.....eeeeeeeeee...eeeeee........eeeeee....eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeee....eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r52 B   2 ALQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain C from PDB  Type:PROTEIN  Length:152
 aligned with P93193_IPOBA | P93193 from UniProtKB/TrEMBL  Length:154

    Alignment length:152
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152  
         P93193_IPOBA     3 LQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
               SCOP domains d3r52c_ C: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.eeeeeee....eeeeee......eeeeeeee.....eeeeeeeeee...eeeeee........eeeee.....eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeee....eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r52 C   3 LQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain D from PDB  Type:PROTEIN  Length:152
 aligned with P93193_IPOBA | P93193 from UniProtKB/TrEMBL  Length:154

    Alignment length:152
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152  
         P93193_IPOBA     3 LQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
               SCOP domains d3r52d_ D: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.eeeeeee....eeeeee......eeeeeeee.....eeeeeeeeee...eeeeee........eeeeee......eeeeeeee....eeeeeeeee....eeeeee....eeeeee....eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r52 D   3 LQLAAHSDARSGPVGSNGGQFWSFRPVRPLNKIVLSFSGSPDQTLNLISITFSSNPTDIITVGGVGPEPLTYTETVNIDGDIIEISGMIANYKGYNVIRSIKFTTNKKEYGPYGANAGTPFNIKIPDGNKIVGFFGNSGWYVDAIGAYYTAK 154
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

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: beta-Prism I (50)

Superfamily: Mannose-binding lectins (42)

Family: automated matches (10)

Protein domain: automated matches (10)

Sweet potato (Ipomoea batatas) [TaxId: 4120] (4)

1a	d3r52a_	A:
1b	d3r52b_	B:
1c	d3r52c_	C:
1d	d3r52d_	D:

(no "CATH Domain" information available for 3R52)

(no "Pfam Domain" information available for 3R52)

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3R52)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asn A:57 - Pro A:58	[ RasMol ]
		Gly A:113 - Pro A:114	[ RasMol ]
		Gly A:14 - Pro A:15	[ RasMol ]
		Gly B:113 - Pro B:114	[ RasMol ]
		Gly B:14 - Pro B:15	[ RasMol ]
		Gly C:113 - Pro C:114	[ RasMol ]
		Gly C:14 - Pro C:15	[ RasMol ]
		Gly D:113 - Pro D:114	[ RasMol ]
		Gly D:14 - Pro D:15	[ RasMol ]

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	3r52
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	P93193_IPOBA \| P93193
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	P93193_IPOBA \| P93193	:	3r50 3r51 4ddn

3r50	APO IPO
3r51	IPO-MMP COMPLEX
3r53	IPO-SIA COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 4)

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