2WQL - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE MAJOR CARROT ALLERGEN DAU C 1

Authors :   Z. Markovic-Housley, A. Basle, S. Padavattan, K. Hoffmann-Sommergru T. Schirmer

Date :   24 Aug 09 (Deposition) - 01 Sep 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (3x)
Biol. Unit 2: C,D  (3x)

Keywords :   Pathogenesis-Related Protein, Allergen, Plant Defense (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Markovic-Housley, A. Basle, S. Padavattan, B. Maderegger, T. Schirmer, K. Hoffmann-Sommergruber
Structure Of The Major Carrot Allergen Dau C 1.
Acta Crystallogr. , Sect. D V. 65 1206 2009
PubMed-ID: 19923716 | Reference-DOI: 10.1107/S0907444909034854

Molecule 1 - MAJOR ALLERGEN DAU C 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDS 56
	Expression System Strain	:	M15
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Common	:	CARROT
	Organism Scientific	:	DAUCUS CAROTA
	Organism Taxid	:	4039
	Synonym	:	CR16, PATHOGENESIS-RELATED PROTEIN GEA20

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 26)

No.	Name	Count	Type	Full Name
1	CL	16	Ligand/Ion	CHLORIDE ION
2	P4C	4	Ligand/Ion	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL
3	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (2, 18)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	P4C	6	Ligand/Ion	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL
3	PEG	12	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	P4C	6	Ligand/Ion	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL
3	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (24, 24)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ILE A:23 , TYR A:39 , THR A:116 , ASN A:140 , LEU A:143	BINDING SITE FOR RESIDUE P4C A 200
02	AC2	SOFTWARE	ILE A:90 , GLN A:139 , ASN A:140	BINDING SITE FOR RESIDUE PEG A 201
03	AC3	SOFTWARE	HIS A:121	BINDING SITE FOR RESIDUE CL A 300
04	AC4	SOFTWARE	SER A:15 , LYS A:18	BINDING SITE FOR RESIDUE CL A 301
05	AC5	SOFTWARE	HIS A:6 , SER A:7	BINDING SITE FOR RESIDUE CL A 302
06	AC6	SOFTWARE	SER A:5	BINDING SITE FOR RESIDUE CL A 303
07	AC7	SOFTWARE	ILE B:23 , TYR B:39 , THR B:116 , ASN B:140 , LEU B:143	BINDING SITE FOR RESIDUE P4C B 200
08	AC8	SOFTWARE	GLN B:139 , ASN B:140	BINDING SITE FOR RESIDUE PEG B 201
09	AC9	SOFTWARE	ASP A:72 , ASN B:75 , GLU B:77	BINDING SITE FOR RESIDUE PEG B 202
10	BC1	SOFTWARE	ASP A:72 , ASP A:82 , HIS A:101 , GLU B:77 , ALA B:78	BINDING SITE FOR RESIDUE PEG B 203
11	BC2	SOFTWARE	HIS B:121	BINDING SITE FOR RESIDUE CL B 300
12	BC3	SOFTWARE	LYS B:18	BINDING SITE FOR RESIDUE CL B 301
13	BC4	SOFTWARE	GLN B:4 , SER B:5	BINDING SITE FOR RESIDUE CL B 303
14	BC5	SOFTWARE	ILE C:23 , TYR C:39 , THR C:116 , ASN C:140 , LEU C:143	BINDING SITE FOR RESIDUE P4C C 200
15	BC6	SOFTWARE	GLN C:139 , ASN C:140	BINDING SITE FOR RESIDUE PEG C 201
16	BC7	SOFTWARE	HIS C:121	BINDING SITE FOR RESIDUE CL C 300
17	BC8	SOFTWARE	SER C:15 , LYS C:18	BINDING SITE FOR RESIDUE CL C 301
18	BC9	SOFTWARE	SER C:7	BINDING SITE FOR RESIDUE CL C 302
19	CC1	SOFTWARE	SER C:5	BINDING SITE FOR RESIDUE CL C 303
20	CC2	SOFTWARE	ILE D:23 , TYR D:39 , THR D:116 , ASN D:140 , LEU D:143	BINDING SITE FOR RESIDUE P4C D 200
21	CC3	SOFTWARE	ILE D:90 , ASN D:140	BINDING SITE FOR RESIDUE PEG D 201
22	CC4	SOFTWARE	HIS D:121	BINDING SITE FOR RESIDUE CL D 300
23	CC5	SOFTWARE	SER D:15 , LYS D:18	BINDING SITE FOR RESIDUE CL D 301
24	CC6	SOFTWARE	HIS D:6	BINDING SITE FOR RESIDUE CL D 302

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

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

Asymmetric Unit (7, 28)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DAU1_DAUCA_001 *	P	36	T	DAU1_DAUCA	---	---	A/B/C/D	T	36	T
2	UniProt	VAR_DAU1_DAUCA_002 *	E	43	D	DAU1_DAUCA	---	---	A/B/C/D	E	43	D
3	UniProt	VAR_DAU1_DAUCA_003 *	S	66	T	DAU1_DAUCA	---	---	A/B/C/D	T	66	T
4	UniProt	VAR_DAU1_DAUCA_004 *	T	80	S	DAU1_DAUCA	---	---	A/B/C/D	S	80	S
5	UniProt	VAR_DAU1_DAUCA_005 *	G	93	E	DAU1_DAUCA	---	---	A/B/C/D	G	93	E
6	UniProt	VAR_DAU1_DAUCA_006 *	L	102	M	DAU1_DAUCA	---	---	A/B/C/D	M	102	M
7	UniProt	VAR_DAU1_DAUCA_007 *	A	138	E	DAU1_DAUCA	---	---	A/B/C/D	A	138	E
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (7, 42)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DAU1_DAUCA_001 *	P	36	T	DAU1_DAUCA	---	---	A/B	T	36	T
2	UniProt	VAR_DAU1_DAUCA_002 *	E	43	D	DAU1_DAUCA	---	---	A/B	E	43	D
3	UniProt	VAR_DAU1_DAUCA_003 *	S	66	T	DAU1_DAUCA	---	---	A/B	T	66	T
4	UniProt	VAR_DAU1_DAUCA_004 *	T	80	S	DAU1_DAUCA	---	---	A/B	S	80	S
5	UniProt	VAR_DAU1_DAUCA_005 *	G	93	E	DAU1_DAUCA	---	---	A/B	G	93	E
6	UniProt	VAR_DAU1_DAUCA_006 *	L	102	M	DAU1_DAUCA	---	---	A/B	M	102	M
7	UniProt	VAR_DAU1_DAUCA_007 *	A	138	E	DAU1_DAUCA	---	---	A/B	A	138	E
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (7, 42)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DAU1_DAUCA_001 *	P	36	T	DAU1_DAUCA	---	---	C/D	T	36	T
2	UniProt	VAR_DAU1_DAUCA_002 *	E	43	D	DAU1_DAUCA	---	---	C/D	E	43	D
3	UniProt	VAR_DAU1_DAUCA_003 *	S	66	T	DAU1_DAUCA	---	---	C/D	T	66	T
4	UniProt	VAR_DAU1_DAUCA_004 *	T	80	S	DAU1_DAUCA	---	---	C/D	S	80	S
5	UniProt	VAR_DAU1_DAUCA_005 *	G	93	E	DAU1_DAUCA	---	---	C/D	G	93	E
6	UniProt	VAR_DAU1_DAUCA_006 *	L	102	M	DAU1_DAUCA	---	---	C/D	M	102	M
7	UniProt	VAR_DAU1_DAUCA_007 *	A	138	E	DAU1_DAUCA	---	---	C/D	A	138	E
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PATHOGENESIS_BETVI	PS00451	Pathogenesis-related proteins Bet v I family signature.	DAU1_DAUCA	88-120	4	A:88-120 B:88-120 C:88-120 D:88-120

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PATHOGENESIS_BETVI	PS00451	Pathogenesis-related proteins Bet v I family signature.	DAU1_DAUCA	88-120	6	A:88-120 B:88-120 - -

Biological Unit 2 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PATHOGENESIS_BETVI	PS00451	Pathogenesis-related proteins Bet v I family signature.	DAU1_DAUCA	88-120	6	- - C:88-120 D:88-120

(no "Exon" information available for 2WQL)

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:152
 aligned with DAU1_DAUCA | O04298 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:152
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152  
           DAU1_DAUCA     3 AQSHSLEITSSVSAEKIFSGIVLDVDTVIPKAAPGAYKSVEVKGDGGAGTVRIITLPEGSPITSMTVRTDAVNKEALTYDSTVIDGDILLGFIESIETHLVVVPTADGGSITKTTAIFHTKGDAVVPEENIKFADAQNTALFKAIEAYLIAN 154
               SCOP domains d2wqla_ A: automated matches                                                                                                                             SCOP domains
               CATH domains 2wqlA00 A:3-154  [code=3.30.530.20, no name defined]                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhh....hhhhhhhhhh.....eeeee.......eeeee........eeeeeeeeee....eeeeeeeeee.....eeeeeeeeeee.......eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------T------D----------------------T-------------S------------E--------M-----------------------------------E---------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------PATHOGENESIS_BETVI  PDB: A:88-120---------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wql A   3 AQSHSLEITSSVSAEKIFSGIVLDVDTVIPKAATGAYKSVEVKGDGGAGTVRIITLPEGSPITTMTVRTDAVNKEALSYDSTVIDGDILLGFIESIETHMVVVPTADGGSITKTTAIFHTKGDAVVPEENIKFADAQNTALFKAIEAYLIAN 154
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with DAU1_DAUCA | O04298 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:152
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152  
           DAU1_DAUCA     3 AQSHSLEITSSVSAEKIFSGIVLDVDTVIPKAAPGAYKSVEVKGDGGAGTVRIITLPEGSPITSMTVRTDAVNKEALTYDSTVIDGDILLGFIESIETHLVVVPTADGGSITKTTAIFHTKGDAVVPEENIKFADAQNTALFKAIEAYLIAN 154
               SCOP domains d2wqlb_ B: automated matches                                                                                                                             SCOP domains
               CATH domains 2wqlB00 B:3-154  [code=3.30.530.20, no name defined]                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhh....hhhhhhhhhh.....eeeee.......eeeee........eeeeeeeeee....eeeeeeeeee.....eeeeeeeeeee.......eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------T------D----------------------T-------------S------------E--------M-----------------------------------E---------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------PATHOGENESIS_BETVI  PDB: B:88-120---------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wql B   3 AQSHSLEITSSVSAEKIFSGIVLDVDTVIPKAATGAYKSVEVKGDGGAGTVRIITLPEGSPITTMTVRTDAVNKEALSYDSTVIDGDILLGFIESIETHMVVVPTADGGSITKTTAIFHTKGDAVVPEENIKFADAQNTALFKAIEAYLIAN 154
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain C from PDB  Type:PROTEIN  Length:152
 aligned with DAU1_DAUCA | O04298 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:152
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152  
           DAU1_DAUCA     3 AQSHSLEITSSVSAEKIFSGIVLDVDTVIPKAAPGAYKSVEVKGDGGAGTVRIITLPEGSPITSMTVRTDAVNKEALTYDSTVIDGDILLGFIESIETHLVVVPTADGGSITKTTAIFHTKGDAVVPEENIKFADAQNTALFKAIEAYLIAN 154
               SCOP domains d2wqlc_ C: automated matches                                                                                                                             SCOP domains
               CATH domains 2wqlC00 C:3-154  [code=3.30.530.20, no name defined]                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhh....hhhhhhhhhh.....eeeee.......eeeee........eeeeeeeeee....eeeeeeeeee.....eeeeeeeeeee.......eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------T------D----------------------T-------------S------------E--------M-----------------------------------E---------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------PATHOGENESIS_BETVI  PDB: C:88-120---------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wql C   3 AQSHSLEITSSVSAEKIFSGIVLDVDTVIPKAATGAYKSVEVKGDGGAGTVRIITLPEGSPITTMTVRTDAVNKEALSYDSTVIDGDILLGFIESIETHMVVVPTADGGSITKTTAIFHTKGDAVVPEENIKFADAQNTALFKAIEAYLIAN 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 DAU1_DAUCA | O04298 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:152
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152  
           DAU1_DAUCA     3 AQSHSLEITSSVSAEKIFSGIVLDVDTVIPKAAPGAYKSVEVKGDGGAGTVRIITLPEGSPITSMTVRTDAVNKEALTYDSTVIDGDILLGFIESIETHLVVVPTADGGSITKTTAIFHTKGDAVVPEENIKFADAQNTALFKAIEAYLIAN 154
               SCOP domains d2wqld_ D: automated matches                                                                                                                             SCOP domains
               CATH domains 2wqlD00 D:3-154  [code=3.30.530.20, no name defined]                                                                                                     CATH domains
           Pfam domains (1) Bet_v_1-2wqlD01 D:3-154                                                                                                                                  Pfam domains (1)
           Pfam domains (2) Bet_v_1-2wqlD02 D:3-154                                                                                                                                  Pfam domains (2)
           Pfam domains (3) Bet_v_1-2wqlD03 D:3-154                                                                                                                                  Pfam domains (3)
           Pfam domains (4) Bet_v_1-2wqlD04 D:3-154                                                                                                                                  Pfam domains (4)
         Sec.struct. author ..eeeeeee...hhhhhhh....hhhhhhhhhh.....eeeee.......eeeee........eeeeeeeeee....eeeeeeeeee.....eeeeeeeeeee.......eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------T------D----------------------T-------------S------------E--------M-----------------------------------E---------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------PATHOGENESIS_BETVI  PDB: D:88-120---------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wql D   3 AQSHSLEITSSVSAEKIFSGIVLDVDTVIPKAATGAYKSVEVKGDGGAGTVRIITLPEGSPITTMTVRTDAVNKEALSYDSTVIDGDILLGFIESIETHMVVVPTADGGSITKTTAIFHTKGDAVVPEENIKFADAQNTALFKAIEAYLIAN 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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: TBP-like (289)

Superfamily: Bet v1-like (158)

Family: Pathogenesis-related protein 10 (PR10)-like (38)

Protein domain: automated matches (9)

Carrot (Daucus carota) [TaxId: 4039] (1)

1a	d2wqla_	A:
1b	d2wqlb_	B:
1c	d2wqlc_	C:
1d	d2wqld_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 (47)

Homologous Superfamily: [code=3.30.530.20, no name defined] (47)

Carrot (Daucus carota) (1)

1a	2wqlA00	A:3-154
1b	2wqlB00	B:3-154
1c	2wqlC00	C:3-154
1d	2wqlD00	D:3-154

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Bet_V_1_like (93)

Family: Bet_v_1 (12)

Daucus carota (Carrot) (1)

1a	Bet_v_1-2wqlD01	D:3-154
1b	Bet_v_1-2wqlD02	D:3-154
1c	Bet_v_1-2wqlD03	D:3-154
1d	Bet_v_1-2wqlD04	D:3-154

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DAU1_DAUCA | O04298)

biological process
	GO:0006952		defense response		Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0009607		response to biotic stimulus		Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism.

Asymmetric Unit
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	Cis Peptide Bonds
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	DAU1_DAUCA \| O04298
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 2WQL)

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 26)

Sites (24, 24)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 28)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (1, 4)

Gene Ontology (2, 2)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File