2F08 - JenaLib

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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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A MAJOR HOUSE DUST MITE ALLERGEN, DERF 2

Authors :   B. Mikami, Y. Tanaka, N. Minato, M. Suzuki, S. Korematsu

Date :   12 Nov 05 (Deposition) - 29 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Immunoglobulin Fold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Suzuki, Y. Tanaka, S. Korematsu, B. Mikami, N. Minato
Crystal Structure And Some Properties Of A Major House Dust Mite Allergen, Derf 2
Biochem. Biophys. Res. Commun. V. 339 679 2006
PubMed-ID: 16313885 | Reference-DOI: 10.1016/J.BBRC.2005.11.065
(for further references see the PDB file header)

Molecule 1 - MITE ALLERGEN DER F II
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ROSSETA(DE3)PLYS
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 1-129
	Organism Common	:	AMERICAN HOUSE DUST MITE
	Organism Scientific	:	DERMATOPHAGOIDES FARINAE
	Organism Taxid	:	6954

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	P4C	1	Ligand/Ion	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	P4C	-1	Ligand/Ion	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	P4C	-1	Ligand/Ion	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	P4C	1	Ligand/Ion	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	P4C	-1	Ligand/Ion	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO B:66 , SER C:57 , GLY C:60 , GLU C:62 , PHE D:75 , THR D:91	BINDING SITE FOR RESIDUE P4C C 400

Asymmetric Unit

No.	Residues
1	A:8	-	A:119
2	A:21	-	A:27
3	A:73	-	A:78
4	B:8	-	B:119
5	B:21	-	B:27
6	B:73	-	B:78
7	C:8	-	C:119
8	C:21	-	C:27
9	C:73	-	C:78
10	D:8	-	D:119
11	D:21	-	D:27
12	D:73	-	D:78

Asymmetric Unit

No.	Residues
1	Cys A:78	-	Pro A:79
2	Cys B:78	-	Pro B:79
3	Cys C:78	-	Pro C:79
4	Cys D:78	-	Pro D:79

Asymmetric Unit (4, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_ALL2_DERFA_001 *	M	93	V	ALL2_DERFA	---	---	A/B/C/D	V	76	V
2	UniProt	VAR_ALL2_DERFA_002 *	I	105	A	ALL2_DERFA	---	---	A/B/C/D	I	88	A
3	UniProt	VAR_ALL2_DERFA_003 *	I	128	V	ALL2_DERFA	---	---	A/B/C/D	I	111	V
4	UniProt	VAR_ALL2_DERFA_004 *	G	142	A	ALL2_DERFA	---	---	A/B/C/D	G	125	A
	* ID not provided by source

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

Biological Unit 1 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_ALL2_DERFA_001 *	M	93	V	ALL2_DERFA	---	---	A	V	76	V
2	UniProt	VAR_ALL2_DERFA_002 *	I	105	A	ALL2_DERFA	---	---	A	I	88	A
3	UniProt	VAR_ALL2_DERFA_003 *	I	128	V	ALL2_DERFA	---	---	A	I	111	V
4	UniProt	VAR_ALL2_DERFA_004 *	G	142	A	ALL2_DERFA	---	---	A	G	125	A
	* ID not provided by source

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

Biological Unit 2 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_ALL2_DERFA_001 *	M	93	V	ALL2_DERFA	---	---	B	V	76	V
2	UniProt	VAR_ALL2_DERFA_002 *	I	105	A	ALL2_DERFA	---	---	B	I	88	A
3	UniProt	VAR_ALL2_DERFA_003 *	I	128	V	ALL2_DERFA	---	---	B	I	111	V
4	UniProt	VAR_ALL2_DERFA_004 *	G	142	A	ALL2_DERFA	---	---	B	G	125	A
	* ID not provided by source

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

Biological Unit 3 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_ALL2_DERFA_001 *	M	93	V	ALL2_DERFA	---	---	C	V	76	V
2	UniProt	VAR_ALL2_DERFA_002 *	I	105	A	ALL2_DERFA	---	---	C	I	88	A
3	UniProt	VAR_ALL2_DERFA_003 *	I	128	V	ALL2_DERFA	---	---	C	I	111	V
4	UniProt	VAR_ALL2_DERFA_004 *	G	142	A	ALL2_DERFA	---	---	C	G	125	A
	* ID not provided by source

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

Biological Unit 4 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_ALL2_DERFA_001 *	M	93	V	ALL2_DERFA	---	---	D	V	76	V
2	UniProt	VAR_ALL2_DERFA_002 *	I	105	A	ALL2_DERFA	---	---	D	I	88	A
3	UniProt	VAR_ALL2_DERFA_003 *	I	128	V	ALL2_DERFA	---	---	D	I	111	V
4	UniProt	VAR_ALL2_DERFA_004 *	G	142	A	ALL2_DERFA	---	---	D	G	125	A
	* ID not provided by source

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

(no "PROSITE Motif" information available for 2F08)

(no "Exon" information available for 2F08)

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:129
 aligned with ALL2_DERFA | Q00855 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:129
                                    27        37        47        57        67        77        87        97       107       117       127       137         
           ALL2_DERFA    18 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFMKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKLIGDNGVLACAIATHGKIRD 146
               SCOP domains d2f08a_ A: Major mite allergen                                                                                                    SCOP domains
               CATH domains 2f08A00 A:1-129  [code=2.60.40.770, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeeeee........eeee....eeeeeeee.......eeeeeeeee..eeee......hhhhh.........eeeeeeee........eeeeeeeeeeee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------V-----------A----------------------V-------------A---- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f08 A   1 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFVKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKLIGDNGVLACAIATHGKIRD 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with ALL2_DERFA | Q00855 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:129
                                    27        37        47        57        67        77        87        97       107       117       127       137         
           ALL2_DERFA    18 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFMKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKLIGDNGVLACAIATHGKIRD 146
               SCOP domains d2f08b_ B: Major mite allergen                                                                                                    SCOP domains
               CATH domains 2f08B00 B:1-129  [code=2.60.40.770, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeeeee........eeee...eeeeeeeee.......eeeeeeeee..eeee......hhhhh.........eeeeeeeee.......eeeeeeeeeeee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------V-----------A----------------------V-------------A---- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f08 B   1 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFVKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKLIGDNGVLACAIATHGKIRD 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:129
 aligned with ALL2_DERFA | Q00855 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:129
                                    27        37        47        57        67        77        87        97       107       117       127       137         
           ALL2_DERFA    18 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFMKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKLIGDNGVLACAIATHGKIRD 146
               SCOP domains d2f08c_ C: Major mite allergen                                                                                                    SCOP domains
               CATH domains 2f08C00 C:1-129  [code=2.60.40.770, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.....eeeeee........eeee...eeeeeeeee.......eeeeeeeee..eeee......hhhhh.........eeeeeeeee.......eeeeeeeeeeee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------V-----------A----------------------V-------------A---- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f08 C   1 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFVKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKLIGDNGVLACAIATHGKIRD 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain D from PDB  Type:PROTEIN  Length:129
 aligned with ALL2_DERFA | Q00855 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:129
                                    27        37        47        57        67        77        87        97       107       117       127       137         
           ALL2_DERFA    18 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFMKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKLIGDNGVLACAIATHGKIRD 146
               SCOP domains d2f08d_ D: Major mite allergen                                                                                                    SCOP domains
               CATH domains 2f08D00 D:1-129  [code=2.60.40.770, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeeeee........eeee...eeeeeeeee.......eeeeeeeee..eeee......hhhhh.........eeeeeeeee.......eeeeeeeeeeee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------V-----------A----------------------V-------------A---- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f08 D   1 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFVKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKLIGDNGVLACAIATHGKIRD 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

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: Immunoglobulin-like beta-sandwich (7299)

Superfamily: E set domains (509)

Family: ML domain (9)

Protein domain: Major mite allergen (7)

House-dust mite (Dermatophagoides farinae), Der f 2 [TaxId: 6954] (5)

1a	d2f08a_	A:
1b	d2f08b_	B:
1c	d2f08c_	C:
1d	d2f08d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.770, no name defined] (9)

American house dust mite (Dermatophagoides farinae) (5)

1a	2f08A00	A:1-129
1b	2f08B00	B:1-129
1c	2f08C00	C:1-129
1d	2f08D00	D:1-129

(no "Pfam Domain" information available for 2F08)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ALL2_DERFA | Q00855)

cellular component
	GO:0005576		extracellular region		The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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		Cys A:78 - Pro A:79	[ RasMol ]
		Cys B:78 - Pro B:79	[ RasMol ]
		Cys C:78 - Pro C:79	[ RasMol ]
		Cys D:78 - Pro D:79	[ RasMol ]

Biological Units
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	2f08
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	ALL2_DERFA \| Q00855
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	ALL2_DERFA \| Q00855	:	1ahk 1ahm 1wrf 1xwv

(no "Related Entries Specified in the PDB File" available for 2F08)

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (12, 12)

Cis Peptide Bonds (4, 4)

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SAPs(SNPs)/Variants (4, 16)

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