1KTJ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   X-RAY STRUCTURE OF DER P 2, THE MAJOR HOUSE DUST MITE ALLERGEN

Authors :   U. Derewenda, J. Li, Z. Derewenda, Z. Dauter, G. A. Mueller, G. S. Rule, D. C. Benjamin

Date :   16 Jan 02 (Deposition) - 15 May 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Allergen, Asthma, X-Ray Structure, Immunoglobulin Fold, Hydrophobic Cavity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. Derewenda, J. Li, Z. Derewenda, Z. Dauter, G. A. Mueller, G. S. Rule, D. C. Benjamin
The Crystal Structure Of A Major Dust Mite Allergen Der P 2, And Its Biological Implications.
J. Mol. Biol. V. 318 189 2002
PubMed-ID: 12054778 | Reference-DOI: 10.1016/S0022-2836(02)00027-X
(for further references see the PDB file header)

Molecule 1 - ALLERGEN DER P 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	EUROPEAN HOUSE DUST MITE
	Organism Scientific	:	DERMATOPHAGOIDES PTERONYSSINUS
	Organism Taxid	:	6956
	Synonym	:	DER P II, DPX

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1KTJ)

(no "Site" information available for 1KTJ)

Asymmetric/Biological 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

Asymmetric/Biological Unit

No.	Residues
1	Cys A:78	-	Pro A:79
2	Cys B:78	-	Pro B:79

Asymmetric/Biological Unit (25, 50)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_ALL2_DERPT_001 *	H	39	A	ALL2_DERPT	---	---	A/B	H	22	A
02	UniProt	VAR_ALL2_DERPT_002 *	G	40	L	ALL2_DERPT	---	---	A/B	G	23	L
03	UniProt	VAR_ALL2_DERPT_003 *	C	44	N	ALL2_DERPT	---	---	A/B	C	27	N
04	UniProt	VAR_ALL2_DERPT_004 *	H	47	S	ALL2_DERPT	---	---	A/B	H	30	S
05	UniProt	VAR_ALL2_DERPT_005 *	G	49	T	ALL2_DERPT	---	---	A/B	G	32	T
06	UniProt	VAR_ALL2_DERPT_006 *	A	56	Y	ALL2_DERPT	---	---	A/B	A	39	Y
07	UniProt	VAR_ALL2_DERPT_007 *	V	57	L	ALL2_DERPT	---	---	A/B	V	40	L
08	UniProt	VAR_ALL2_DERPT_008 *	N	61	L	ALL2_DERPT	---	---	A/B	N	44	L
09	UniProt	VAR_ALL2_DERPT_009 *	T	64	S	ALL2_DERPT	---	---	A/B	T	47	S
10	UniProt	VAR_ALL2_DERPT_010 *	I	75	Y	ALL2_DERPT	---	---	A/B	I	58	Y
11	UniProt	VAR_ALL2_DERPT_011 *	L	78	C	ALL2_DERPT	---	---	A/B	L	61	C
12	UniProt	VAR_ALL2_DERPT_012 *	D	81	V	ALL2_DERPT	---	---	A/B	D	64	V
13	UniProt	VAR_ALL2_DERPT_013 *	C	95	P	ALL2_DERPT	---	---	A/B	C	78	P
14	UniProt	VAR_ALL2_DERPT_014 *	V	98	T	ALL2_DERPT	---	---	A/B	V	81	T
15	UniProt	VAR_ALL2_DERPT_015 *	T	108	V	ALL2_DERPT	---	---	A/B	T	91	V
16	UniProt	VAR_ALL2_DERPT_016 *	V	111	L	ALL2_DERPT	---	---	A/B	V	94	L
17	UniProt	VAR_ALL2_DERPT_017 *	I	114	N	ALL2_DERPT	---	---	A/B	I	97	N
18	UniProt	VAR_ALL2_DERPT_018 *	A	115	T	ALL2_DERPT	---	---	A/B	A	98	T
19	UniProt	VAR_ALL2_DERPT_019 *	P	116	A	ALL2_DERPT	---	---	A/B	P	99	A
20	UniProt	VAR_ALL2_DERPT_020 *	S	118	A	ALL2_DERPT	---	---	A/B	S	101	A
21	UniProt	VAR_ALL2_DERPT_021 *	V	127	L	ALL2_DERPT	---	---	A/B	V	110	L
22	UniProt	VAR_ALL2_DERPT_022 *	M	128	L	ALL2_DERPT	---	---	A/B	M	111	L
23	UniProt	VAR_ALL2_DERPT_023 *	D	131	N	ALL2_DERPT	---	---	A/B	D	114	N
24	UniProt	VAR_ALL2_DERPT_024 *	V	133	A	ALL2_DERPT	---	---	A/B	V	116	A
25	UniProt	VAR_ALL2_DERPT_025 *	I	144	L	ALL2_DERPT	---	---	A/B	I	127	L
	* ID not provided by source

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

(no "PROSITE Motif" information available for 1KTJ)

(no "Exon" information available for 1KTJ)

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:129
 aligned with ALL2_DERPT | P49278 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:129
                                    27        37        47        57        67        77        87        97       107       117       127       137         
           ALL2_DERPT    18 DQVDVKDCANHEIKKVLVPGCHGSEPCIIHRGKPFQLEAVFEANQNTKTAKIEIKASIDGLEVDVPGIDPNACHYMKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKVMGDDGVLACAIATHAKIRD 146
               SCOP domains d1ktja_ A: Major mite allergen                                                                                                    SCOP domains
               CATH domains 1ktjA00 A:1-129  [code=2.60.40.770, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeeee.........eeee...eeeeeeeee........eeeeeeee..eee.......hhhhh.........eeeeeeeee..........eeeeeeeee..eeeeeeee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------AL---N--S-T------YL---L--S----------Y--C--V-------------P--T---------V--L--NTA-A--------LL--N-A----------L-- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ktj A   1 SEVDVKDCANHEIKKVLVPGCHGSEPCIIHRGKPFQLEAVFEANQNTKTAKIEIKASIDGLEVDVPGIDPNACHYMKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKVMGDDGVLACAIATHAKIRD 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with ALL2_DERPT | P49278 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:129
                                    27        37        47        57        67        77        87        97       107       117       127       137         
           ALL2_DERPT    18 DQVDVKDCANHEIKKVLVPGCHGSEPCIIHRGKPFQLEAVFEANQNTKTAKIEIKASIDGLEVDVPGIDPNACHYMKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKVMGDDGVLACAIATHAKIRD 146
               SCOP domains d1ktjb_ B: Major mite allergen                                                                                                    SCOP domains
               CATH domains 1ktjB00 B:1-129  [code=2.60.40.770, no name defined]                                                                              CATH domains
           Pfam domains (1) --E1_DerP2_DerF2-1ktjB01 B:3-126                                                                                              --- Pfam domains (1)
           Pfam domains (2) --E1_DerP2_DerF2-1ktjB02 B:3-126                                                                                              --- Pfam domains (2)
         Sec.struct. author .....ee.....eeeee.........eeee...eeeeeeeee........eeeeeeee..eee.......hhhhhh........eeeeeeeee..........eeeeeeeee..eeeeeeee..eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------AL---N--S-T------YL---L--S----------Y--C--V-------------P--T---------V--L--NTA-A--------LL--N-A----------L-- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ktj B   1 SEVDVKDCANHEIKKVLVPGCHGSEPCIIHRGKPFQLEAVFEANQNTKTAKIEIKASIDGLEVDVPGIDPNACHYMKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKVMGDDGVLACAIATHAKIRD 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/Biological 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 pteronyssinus), Der p 2 [TaxId: 6956] (2)

1a	d1ktja_	A:
1b	d1ktjb_	B:

Asymmetric/Biological 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)

European house dust mite (Dermatophagoides pteronyssinus) (2)

1a	1ktjA00	A:1-129
1b	1ktjB00	B:1-129

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: E1_DerP2_DerF2] (8)

Family: E1_DerP2_DerF2 (8)

Dermatophagoides pteronyssinus (European house dust mite) (1)

1a	E1_DerP2_DerF2-1ktjB01	B:3-126
1b	E1_DerP2_DerF2-1ktjB02	B:3-126

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ALL2_DERPT | P49278)

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/Biological Unit
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	Cis Peptide Bonds
		Cys A:78 - Pro A:79	[ RasMol ]
		Cys B:78 - Pro B:79	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

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