2AS8 - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF MATURE AND FULLY ACTIVE DER P 1 ALLERGEN

Authors :   S. De Halleux, E. Stura, L. Vanderelst, V. Carlier, M. Jacquemin, J. - M. Saint-Remy

Date :   23 Aug 05 (Deposition) - 06 Dec 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Cysteine Proteinase Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. De Halleux, E. Stura, L. Vanderelst, V. Carlier, M. Jacquemin, J. -M. Saint-Remy
Three-Dimensional Structure And Ige-Binding Properties Of Mature Fully Active Der P 1, A Clinically Relevant Major Allergen
J. Allergy Clin. Immunol. V. 117 571 2006
PubMed-ID: 16522455 | Reference-DOI: 10.1016/J.JACI.2005.11.032
(for further references see the PDB file header)

Molecule 1 - MAJOR MITE FECAL ALLERGEN DER P 1
	Chains	:	A, B
	EC Number	:	3.4.22.-
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPICZ C
	Expression System Strain	:	X-33
	Expression System Taxid	:	4922
	Expression System Vector	:	PCR4-BLUNT
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	EUROPEAN HOUSE DUST MITE
	Organism Scientific	:	DERMATOPHAGOIDES PTERONYSSINUS
	Organism Taxid	:	6956
	Synonym	:	DER P I

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:56 , LEU A:57 , GLU A:59 , GLU A:91 , HOH A:1027 , HOH A:1264	BINDING SITE FOR RESIDUE MG A 1001
2	AC2	SOFTWARE	ASP B:56 , LEU B:57 , GLU B:59 , GLU B:91 , HOH B:2041 , HOH B:2081	BINDING SITE FOR RESIDUE MG B 2001

Asymmetric/Biological Unit

No.	Residues
1	A:4	-	A:117
2	A:31	-	A:71
3	A:65	-	A:103
4	B:4	-	B:117
5	B:31	-	B:71
6	B:65	-	B:103

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:120	-	Pro A:121
2	Tyr B:120	-	Pro B:121

Asymmetric/Biological Unit (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PEPT1_DERPT_001 *	Y	148	H	PEPT1_DERPT	---	---	A/B	Y	50	H
2	UniProt	VAR_PEPT1_DERPT_002 *	E	179	K	PEPT1_DERPT	---	---	A/B	E	81	K
3	UniProt	VAR_PEPT1_DERPT_003 *	V	222	A	PEPT1_DERPT	---	---	A/B	A	124	A
4	UniProt	VAR_PEPT1_DERPT_004 *	S	234	T	PEPT1_DERPT	---	---	A/B	S	136	T
5	UniProt	VAR_PEPT1_DERPT_005 *	E	313	Q	PEPT1_DERPT	---	---	A/B	E	215	Q
	* ID not provided by source

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

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	PEPT1_DERPT	126-137	2	A:28-39 B:28-39
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	PEPT1_DERPT	266-276	2	A:168-178 B:168-178
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	PEPT1_DERPT	283-302	2	A:185-204 B:185-204

(no "Exon" information available for 2AS8)

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:222
 aligned with PEPT1_DERPT | P08176 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:222
                                   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318  
          PEPT1_DERPT    99 TNACSINGNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNQSLDLAEQELVDCASQHGCHGDTIPRGIEYIQHNGVVQESYYRYVAREQSCRRPNAQRFGISNYCQIYPPNVNKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNYHAVNIVGYSNAQGVDYWIVRNSWDTNWGDNGYGYFAANIDLMMIEEYPYVVIL 320
               SCOP domains d2as8a1 A:1-222 Major mite fecal allergen der p 1                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eehhhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh........hhhhhhhhhhhhh..hhhhh....................eeee....hhhhhhhhhhhhh..eeeeeee.hhhhhhhh..............eeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------H------------------------------K------------------------------------------A-----------T------------------------------------------------------------------------------Q------- SAPs(SNPs)
                    PROSITE ---------------------------THIOL_PROTEA--------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  ------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2as8 A   1 TNACSINGNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRQQSLDLAEQELVDCASQHGCHGDTIPRGIEYIQHNGVVQESYYRYVAREQSCRRPNAQRFGISNYCQIYPPNANKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNYHAVNIVGYSNAQGVDYWIVRNSWDTNWGDNGYGYFAANIDLMMIEEYPYVVIL 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:222
 aligned with PEPT1_DERPT | P08176 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:222
                                   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318  
          PEPT1_DERPT    99 TNACSINGNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNQSLDLAEQELVDCASQHGCHGDTIPRGIEYIQHNGVVQESYYRYVAREQSCRRPNAQRFGISNYCQIYPPNVNKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNYHAVNIVGYSNAQGVDYWIVRNSWDTNWGDNGYGYFAANIDLMMIEEYPYVVIL 320
               SCOP domains d2as8b_ B: Major mite fecal allergen der p 1                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eehhhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhh.hhhhhhhhhhhhh..hhhhh....................eeee....hhhhhhhhhhhhh..eeeeeee.hhhhhhh...............eeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------H------------------------------K------------------------------------------A-----------T------------------------------------------------------------------------------Q------- SAPs(SNPs)
                    PROSITE ---------------------------THIOL_PROTEA--------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  ------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2as8 B   1 TNACSINGNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRQQSLDLAEQELVDCASQHGCHGDTIPRGIEYIQHNGVVQESYYRYVAREQSCRRPNAQRFGISNYCQIYPPNANKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNYHAVNIVGYSNAQGVDYWIVRNSWDTNWGDNGYGYFAANIDLMMIEEYPYVVIL 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

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

Fold: Cysteine proteinases (392)

Superfamily: Cysteine proteinases (392)

Family: Papain-like (200)

Protein domain: Major mite fecal allergen der p 1 (3)

House-dust mite (Dermatophagoides pteronyssinus) [TaxId: 6956] (3)

1a	d2as8a1	A:1-222
1b	d2as8b_	B:

(no "CATH Domain" information available for 2AS8)

(no "Pfam Domain" information available for 2AS8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PEPT1_DERPT | P08176)

molecular function
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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
		Tyr A:120 - Pro A:121	[ RasMol ]
		Tyr B:120 - Pro B:121	[ RasMol ]

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	2as8
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	3.4.22.-
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	PEPT1_DERPT \| P08176	:	1xkg 3rvw 3rvx 4pp1 4pp2 5vph

(no "Related Entries Specified in the PDB File" available for 2AS8)

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

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Exons (0, 0)

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