2DPF - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CURCULIN1 HOMODIMER

Authors :   E. Kurimoto, M. Suzuki, E. Amemiya, Y. Yamaguchi, S. Nirasawa, N. Shimb T. Kashiwagi, M. Kawai, E. Suzuki, K. Kato

Date :   11 May 06 (Deposition) - 15 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Sweet Taste, Taste Modifying, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Kurimoto, M. Suzuki, E. Amemiya, Y. Yamaguchi, S. Nirasawa, N. Shimba, N. Xu, T. Kashiwagi, M. Kawai, E. Suzuki, K. Kato
Curculin Exhibits Sweet-Tasting And Taste-Modifying Activities Through Its Distinct Molecular Surfaces.
J. Biol. Chem. V. 282 33252 2007
PubMed-ID: 17895249 | Reference-DOI: 10.1074/JBC.C700174200

Molecule 1 - CURCULIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	LUMBAH
	Organism Scientific	:	CURCULIGO LATIFOLIA
	Organism Taxid	:	4676

		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 (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS C:83 , GLN D:89 , ASP D:91 , ARG D:93 , HOH D:679 , HOH D:683	BINDING SITE FOR RESIDUE SO4 D 601
2	AC2	SOFTWARE	ASP C:13 , ASN C:27 , HOH C:626 , HOH C:702	BINDING SITE FOR RESIDUE SO4 C 602
3	AC3	SOFTWARE	HIS D:11 , HOH D:632 , HOH D:695 , HOH D:714	BINDING SITE FOR RESIDUE SO4 D 603

Asymmetric Unit

No.	Residues
1	A:29	-	A:52
2	A:77	-	B:109
3	A:109	-	B:77
4	B:29	-	B:52
5	C:29	-	C:52
6	C:77	-	D:109
7	C:109	-	D:77
8	D:29	-	D:52

Asymmetric Unit

No.	Residues
1	Gly A:98	-	Pro A:99
2	Gly B:98	-	Pro B:99
3	Gly C:98	-	Pro C:99
4	Gly D:98	-	Pro D:99

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BULB_LECTIN	PS50927	Bulb-type lectin domain profile.	CURC1_MOLLA	23-131	4	A:1-109 B:1-109 C:1-109 D:1-109

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BULB_LECTIN	PS50927	Bulb-type lectin domain profile.	CURC1_MOLLA	23-131	2	A:1-109 B:1-109 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BULB_LECTIN	PS50927	Bulb-type lectin domain profile.	CURC1_MOLLA	23-131	2	- - C:1-109 D:1-109

(no "Exon" information available for 2DPF)

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:111
 aligned with CURC1_MOLLA | P19667 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:111
                                    32        42        52        62        72        82        92       102       112       122       132 
          CURC1_MOLLA    23 DNVLLSGQTLHADHSLQAGAYTLTIQNKCNLVKYQNGRQIWASNTDRRGSGCRLTLLSDGNLVIYDHNNNDVWGSACWGDNGKYALVLQKDGRFVIYGPVLWSLGPNGCRR 133
               SCOP domains d2dpfa_ A: automated matches                                                                                    SCOP domains
               CATH domains 2dpfA00 A:1-111 Agglutinin, subunit A                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee..eeeee..eeeee.....eeeee..eeeee..........eeee.....eeee.....eeee..........eeee.....eeee..eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE BULB_LECTIN  PDB: A:1-109 UniProt: 23-131                                                                    -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 2dpf A   1 DNVLLSGQTLHADHSLQAGAYTLTIQNKCNLVKYQNGRQIWASNTDRRGSGCRLTLLSDGNLVIYDHNNNDVWGSACWGDNGKYALVLQKDGRFVIYGPVLWSLGPNGCRR 111
                                    10        20        30        40        50        60        70        80        90       100       110

Chain B from PDB  Type:PROTEIN  Length:111
 aligned with CURC1_MOLLA | P19667 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:111
                                    32        42        52        62        72        82        92       102       112       122       132 
          CURC1_MOLLA    23 DNVLLSGQTLHADHSLQAGAYTLTIQNKCNLVKYQNGRQIWASNTDRRGSGCRLTLLSDGNLVIYDHNNNDVWGSACWGDNGKYALVLQKDGRFVIYGPVLWSLGPNGCRR 133
               SCOP domains d2dpfb_ B: automated matches                                                                                    SCOP domains
               CATH domains 2dpfB00 B:1-111 Agglutinin, subunit A                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...ee....eeee..eeeee.....eeeee..eeeee..........eeee.....eeee.....eeee..........eeee.....eeee..eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE BULB_LECTIN  PDB: B:1-109 UniProt: 23-131                                                                    -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 2dpf B   1 DNVLLSGQTLHADHSLQAGAYTLTIQNKCNLVKYQNGRQIWASNTDRRGSGCRLTLLSDGNLVIYDHNNNDVWGSACWGDNGKYALVLQKDGRFVIYGPVLWSLGPNGCRR 111
                                    10        20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:PROTEIN  Length:111
 aligned with CURC1_MOLLA | P19667 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:111
                                    32        42        52        62        72        82        92       102       112       122       132 
          CURC1_MOLLA    23 DNVLLSGQTLHADHSLQAGAYTLTIQNKCNLVKYQNGRQIWASNTDRRGSGCRLTLLSDGNLVIYDHNNNDVWGSACWGDNGKYALVLQKDGRFVIYGPVLWSLGPNGCRR 133
               SCOP domains d2dpfc_ C: automated matches                                                                                    SCOP domains
               CATH domains 2dpfC00 C:1-111 Agglutinin, subunit A                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee..eeeee..eeeee.....eeeee..eeeee..........eeee.....eeee.....eeee..........eeee.....eeee..eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE BULB_LECTIN  PDB: C:1-109 UniProt: 23-131                                                                    -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 2dpf C   1 DNVLLSGQTLHADHSLQAGAYTLTIQNKCNLVKYQNGRQIWASNTDRRGSGCRLTLLSDGNLVIYDHNNNDVWGSACWGDNGKYALVLQKDGRFVIYGPVLWSLGPNGCRR 111
                                    10        20        30        40        50        60        70        80        90       100       110

Chain D from PDB  Type:PROTEIN  Length:111
 aligned with CURC1_MOLLA | P19667 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:111
                                    32        42        52        62        72        82        92       102       112       122       132 
          CURC1_MOLLA    23 DNVLLSGQTLHADHSLQAGAYTLTIQNKCNLVKYQNGRQIWASNTDRRGSGCRLTLLSDGNLVIYDHNNNDVWGSACWGDNGKYALVLQKDGRFVIYGPVLWSLGPNGCRR 133
               SCOP domains d2dpfd_ D: automated matches                                                                                    SCOP domains
               CATH domains 2dpfD00 D:1-111 Agglutinin, subunit A                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...ee...eeeee..eeeee.....eeeee..eeeee..........eeee.....eeee.....eeee..........eeee.....eeee..eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE BULB_LECTIN  PDB: D:1-109 UniProt: 23-131                                                                    -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 2dpf D   1 DNVLLSGQTLHADHSLQAGAYTLTIQNKCNLVKYQNGRQIWASNTDRRGSGCRLTLLSDGNLVIYDHNNNDVWGSACWGDNGKYALVLQKDGRFVIYGPVLWSLGPNGCRR 111
                                    10        20        30        40        50        60        70        80        90       100       110

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: beta-Prism II (19)

Superfamily: alpha-D-mannose-specific plant lectins (19)

Family: automated matches (7)

Protein domain: automated matches (7)

Curculigo latifolia [TaxId: 4676] (2)

1a	d2dpfa_	A:
1b	d2dpfb_	B:
1c	d2dpfc_	C:
1d	d2dpfd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Orthogonal Prism (16)

Topology: Agglutinin, subunit A (16)

Homologous Superfamily: Agglutinin, subunit A (16)

Lumbah (Curculigo latifolia) (2)

1a	2dpfA00	A:1-111
1b	2dpfB00	B:1-111
1c	2dpfC00	C:1-111
1d	2dpfD00	D:1-111

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CURC1_MOLLA | P19667)

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:98 - Pro A:99	[ RasMol ]
		Gly B:98 - Pro B:99	[ RasMol ]
		Gly C:98 - Pro C:99	[ RasMol ]
		Gly D:98 - Pro D:99	[ RasMol ]

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	2dpf
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	CURC1_MOLLA \| P19667	:	2d04

(no "Related Entries Specified in the PDB File" available for 2DPF)

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (8, 8)

Cis Peptide Bonds (4, 4)

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