2OPO - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE CALCIUM-BINDING POLLEN ALLERGEN CHE A 3

Authors :   P. Verdino, W. Keller

Date :   29 Jan 07 (Deposition) - 06 Feb 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Calcium-Binding Protein, Dimer, Domain-Swapping, Ef-Hand, Allergen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Verdino, R. Barderas, M. Villalba, K. Westritschnig, R. Valenta, R. Rodriguez, W. Keller
Three-Dimensional Structure Of The Cross-Reactive Pollen Allergen Che A 3: Visualizing Cross-Reactivity On The Molecular Surfaces Of Weed, Grass, And Tree Pollen Allergens.
J. Immunol. V. 180 2313 2008
PubMed-ID: 18250440
(for further references see the PDB file header)

Molecule 1 - POLCALCIN CHE A 3
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-11B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	CHENOPODIUM ALBUM
	Organism Taxid	:	3559
	Synonym	:	CALCIUM-BINDING POLLEN ALLERGEN CHE A 3

		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 (2, 12)

No.	Name	Count	Type	Full Name
1	CA	8	Ligand/Ion	CALCIUM ION
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:21 , ASN A:23 , ASP A:25 , LYS A:27 , GLU A:32 , HOH A:303	BINDING SITE FOR RESIDUE CA A 301
02	AC2	SOFTWARE	ASP A:56 , ASP A:58 , ASP A:60 , PHE A:62 , GLU A:67 , HOH A:304	BINDING SITE FOR RESIDUE CA A 302
03	AC3	SOFTWARE	ASP B:21 , ASN B:23 , ASP B:25 , LYS B:27 , GLU B:32 , HOH B:405	BINDING SITE FOR RESIDUE CA B 303
04	AC4	SOFTWARE	ASP B:56 , ASP B:58 , ASP B:60 , PHE B:62 , GLU B:67 , HOH B:406	BINDING SITE FOR RESIDUE CA B 304
05	AC5	SOFTWARE	ARG A:50 , ARG B:49 , ARG B:50	BINDING SITE FOR RESIDUE SO4 B 401
06	AC6	SOFTWARE	THR A:6 , ASP A:9 , ARG A:13 , ARG B:73 , ARG B:76 , LYS D:38	BINDING SITE FOR RESIDUE SO4 B 404
07	AC7	SOFTWARE	ASP C:21 , ASN C:23 , ASP C:25 , LYS C:27 , GLU C:32 , HOH C:404	BINDING SITE FOR RESIDUE CA C 305
08	AC8	SOFTWARE	ASP C:56 , ASP C:58 , ASP C:60 , PHE C:62 , GLU C:67 , HOH C:405	BINDING SITE FOR RESIDUE CA C 306
09	AC9	SOFTWARE	ASP C:58 , SER C:64 , ASP C:66 , HOH C:407 , HOH C:440 , HOH C:488	BINDING SITE FOR RESIDUE SO4 C 402
10	BC1	SOFTWARE	ARG C:15 , ARG C:19 , HOH C:406 , HOH C:435 , HOH C:455 , HOH D:327	BINDING SITE FOR RESIDUE SO4 C 403
11	BC2	SOFTWARE	ASP D:21 , ASN D:23 , ASP D:25 , LYS D:27 , GLU D:32 , HOH D:309	BINDING SITE FOR RESIDUE CA D 307
12	BC3	SOFTWARE	ASP D:56 , ASP D:58 , ASP D:60 , PHE D:62 , GLU D:67 , HOH D:310	BINDING SITE FOR RESIDUE CA D 308

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

(no "Cis Peptide Bond" information available for 2OPO)

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

Asymmetric Unit (2, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	POLC3_CHEAL	8-43 46-78	8	A:8-43 B:8-43 C:8-43 D:8-43 A:46-78 B:46-78 C:46-78 D:46-78
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	POLC3_CHEAL	21-33 56-68	8	A:21-33 B:21-33 C:21-33 D:21-33 A:56-68 B:56-68 C:56-68 D:56-68

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	POLC3_CHEAL	8-43 46-78	4	A:8-43 B:8-43 - - A:46-78 B:46-78 - -
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	POLC3_CHEAL	21-33 56-68	4	A:21-33 B:21-33 - - A:56-68 B:56-68 - -

Biological Unit 2 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	POLC3_CHEAL	8-43 46-78	4	- - C:8-43 D:8-43 - - C:46-78 D:46-78
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	POLC3_CHEAL	21-33 56-68	4	- - C:21-33 D:21-33 - - C:56-68 D:56-68

(no "Exon" information available for 2OPO)

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:81
 aligned with POLC3_CHEAL | Q84V36 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:81
                                    15        25        35        45        55        65        75        85 
           POLC3_CHEAL    6 TPQDIADRERIFKRFDTNGDGKISSSELGDALKTLGSVTPDEVRRMMAEIDTDGDGFISFDEFTDFARANRGLVKDVSKIF 86
               SCOP domains d2opoa_ A: Polcalcin Che a 3                                                      SCOP domains
               CATH domains 2opoA00 A:6-86 EF-hand                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.....eeehhhhhhhhhh....hhhhhhhhhhhhh.....eehhhhhhhhhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --EF_HAND_2  PDB: A:8-43 UniProt: 8-43--EF_HAND_2  PDB: A:46-78          -------- PROSITE (1)
                PROSITE (2) ---------------EF_HAND_1    ----------------------EF_HAND_1    ------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------- Transcript
                  2opo A  6 TPQDIADRERIFKRFDTNGDGKISSSELGDALKTLGSVTPDEVRRMMAEIDTDGDGFISFDEFTDFARANRGLVKDVSKIF 86
                                    15        25        35        45        55        65        75        85

Chain B from PDB  Type:PROTEIN  Length:81
 aligned with POLC3_CHEAL | Q84V36 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:81
                                    15        25        35        45        55        65        75        85 
           POLC3_CHEAL    6 TPQDIADRERIFKRFDTNGDGKISSSELGDALKTLGSVTPDEVRRMMAEIDTDGDGFISFDEFTDFARANRGLVKDVSKIF 86
               SCOP domains d2opob_ B: Polcalcin Che a 3                                                      SCOP domains
               CATH domains 2opoB00 B:6-86 EF-hand                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --EF_HAND_2  PDB: B:8-43 UniProt: 8-43--EF_HAND_2  PDB: B:46-78          -------- PROSITE (1)
                PROSITE (2) ---------------EF_HAND_1    ----------------------EF_HAND_1    ------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------- Transcript
                  2opo B  6 TPQDIADRERIFKRFDTNGDGKISSSELGDALKTLGSVTPDEVRRMMAEIDTDGDGFISFDEFTDFARANRGLVKDVSKIF 86
                                    15        25        35        45        55        65        75        85

Chain C from PDB  Type:PROTEIN  Length:85
 aligned with POLC3_CHEAL | Q84V36 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:85
                                    11        21        31        41        51        61        71        81     
           POLC3_CHEAL    2 AAEDTPQDIADRERIFKRFDTNGDGKISSSELGDALKTLGSVTPDEVRRMMAEIDTDGDGFISFDEFTDFARANRGLVKDVSKIF 86
               SCOP domains d2opoc_ C: Polcalcin Che a 3                                                          SCOP domains
               CATH domains 2opoC00 C:2-86 EF-hand                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------EF_HAND_2  PDB: C:8-43 UniProt: 8-43--EF_HAND_2  PDB: C:46-78          -------- PROSITE (1)
                PROSITE (2) -------------------EF_HAND_1    ----------------------EF_HAND_1    ------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  2opo C  2 AAEDTPQDIADRERIFKRFDTNGDGKISSSELGDALKTLGSVTPDEVRRMMAEIDTDGDGFISFDEFTDFARANRGLVKDVSKIF 86
                                    11        21        31        41        51        61        71        81

Chain D from PDB  Type:PROTEIN  Length:82
 aligned with POLC3_CHEAL | Q84V36 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:82
                                    14        24        34        44        54        64        74        84  
           POLC3_CHEAL    5 DTPQDIADRERIFKRFDTNGDGKISSSELGDALKTLGSVTPDEVRRMMAEIDTDGDGFISFDEFTDFARANRGLVKDVSKIF 86
               SCOP domains d2opod_ D: Polcalcin Che a 3                                                       SCOP domains
               CATH domains 2opoD00 D:5-86 EF-hand                                                             CATH domains
           Pfam domains (1) ------EF_hand_5-2opoD01 D:11-72                                     -------------- Pfam domains (1)
           Pfam domains (2) ------EF_hand_5-2opoD02 D:11-72                                     -------------- Pfam domains (2)
           Pfam domains (3) ------EF_hand_5-2opoD03 D:11-72                                     -------------- Pfam domains (3)
           Pfam domains (4) ------EF_hand_5-2opoD04 D:11-72                                     -------------- Pfam domains (4)
           Pfam domains (5) -----------------------EF_hand_6-2opoD05 D:28-75                       ----------- Pfam domains (5)
           Pfam domains (6) -----------------------EF_hand_6-2opoD06 D:28-75                       ----------- Pfam domains (6)
           Pfam domains (7) -----------------------EF_hand_6-2opoD07 D:28-75                       ----------- Pfam domains (7)
           Pfam domains (8) -----------------------EF_hand_6-2opoD08 D:28-75                       ----------- Pfam domains (8)
         Sec.struct. author .hhhhhhhhhhhhhhhh......eehhhhhhhhhhhh..hhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---EF_HAND_2  PDB: D:8-43 UniProt: 8-43--EF_HAND_2  PDB: D:46-78          -------- PROSITE (1)
                PROSITE (2) ----------------EF_HAND_1    ----------------------EF_HAND_1    ------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------- Transcript
                  2opo D  5 DTPQDIADRERIFKRFDTNGDGKISSSELGDALKTLGSVTPDEVRRMMAEIDTDGDGFISFDEFTDFARANRGLVKDVSKIF 86
                                    14        24        34        44        54        64        74        84

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 alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: Polcalcin (6)

Protein domain: Polcalcin Che a 3 (1)

Pigweed (Chenopodium album) [TaxId: 3559] (1)

1a	d2opoa_	A:
1b	d2opob_	B:
1c	d2opoc_	C:
1d	d2opod_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Chenopodium album. Organism_taxid: 3559. (1)

1a	2opoC00	C:2-86
1b	2opoD00	D:5-86
1c	2opoA00	A:6-86
1d	2opoB00	B:6-86

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EF_hand (270)

Family: EF_hand_5 (126)

Chenopodium album (Lambs-quarters) (1)

1a	EF_hand_5-2opoD01	D:11-72
1b	EF_hand_5-2opoD02	D:11-72
1c	EF_hand_5-2opoD03	D:11-72
1d	EF_hand_5-2opoD04	D:11-72

Family: EF_hand_6 (75)

Chenopodium album (Lambs-quarters) (1)

2a	EF_hand_6-2opoD05	D:28-75
2b	EF_hand_6-2opoD06	D:28-75
2c	EF_hand_6-2opoD07	D:28-75
2d	EF_hand_6-2opoD08	D:28-75

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (POLC3_CHEAL | Q84V36)

molecular function
	GO:0005509		calcium ion binding		Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.

Asymmetric Unit
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Description

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Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

SS Bonds (0, 0)

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