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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE MAJOR HOUSE DUST MITE ALLERGEN DER P 1 IN ITS PRO FORM AT 1.61 A RESOLUTION

Authors :   K. Meno, P. B. Thorsted, M. Gajhede

Date :   29 Sep 04 (Deposition) - 28 Jun 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.61

Chains :   Asym./Biol. Unit : A

Keywords :   Major Allergen, Cysteine Protease, House Dust Mite, Dermatophagoides Pteronyssinus, Inactive Mutant, Pro Peptide, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Meno, P. B. Thorsted, H. Ipsen, O. Kristensen, J. N. Larsen, M. D. Spangfort, M. Gajhede, K. Lund
The Crystal Structure Of Recombinant Proder P 1, A Major House Dust Mite Proteolytic Allergen.
J. Immunol. V. 175 3835 2005
PubMed-ID: 16148130

Molecule 1 - MAJOR MITE FECAL ALLERGEN DER P 1
	Chains	:	A
	EC Number	:	3.4.22.-
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PGAPZALPHAA
	Expression System Strain	:	X33
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 19-320
	Gene	:	DERP1
	Mutation	:	YES
	Organism Common	:	EUROPEAN HOUSE DUST MITE
	Organism Scientific	:	DERMATOPHAGOIDES PTERONYSSINUS
	Organism Taxid	:	6956
	Synonym	:	DER P I

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION
3	YT3	1	Ligand/Ion	YTTRIUM (III) ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:136 , LEU A:137 , GLU A:139 , GLU A:171 , HOH A:603 , HOH A:604 , HOH A:607 , HOH A:614	BINDING SITE FOR RESIDUE YT3 A 401
2	AC2	SOFTWARE	ARG A:106 , MET A:107 , PHE A:117 , ASN A:205 , HOH A:603 , HOH A:604 , HOH A:607 , HOH A:629 , HOH A:642 , HOH A:693 , HOH A:913	BINDING SITE FOR RESIDUE SO4 A 501
3	AC3	SOFTWARE	SER A:182 , ARG A:184 , GLY A:303 , GLN A:304 , HOH A:839 , HOH A:863	BINDING SITE FOR RESIDUE SO4 A 502
4	AC4	SOFTWARE	GLN A:170 , SER A:172 , GLN A:240 , ASP A:264 , ALA A:285 , ALA A:286 , HOH A:650 , HOH A:651	BINDING SITE FOR RESIDUE GOL A 601
5	AC5	SOFTWARE	MET A:63 , PHE A:75 , ALA A:114 , TRP A:115 , GLY A:153 , ASP A:154 , ILE A:221 , HIS A:250 , ALA A:251	BINDING SITE FOR RESIDUE GOL A 602

Asymmetric/Biological Unit

No.	Residues
1	A:84	-	A:197
2	A:111	-	A:151
3	A:145	-	A:183

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:200	-	Pro A:201

Asymmetric/Biological Unit (5, 5)

								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	Y	130	H
2	UniProt	VAR_PEPT1_DERPT_002 *	E	179	K	PEPT1_DERPT	---	---	A	E	161	K
3	UniProt	VAR_PEPT1_DERPT_003 *	V	222	A	PEPT1_DERPT	---	---	A	A	204	A
4	UniProt	VAR_PEPT1_DERPT_004 *	S	234	T	PEPT1_DERPT	---	---	A	S	216	T
5	UniProt	VAR_PEPT1_DERPT_005 *	E	313	Q	PEPT1_DERPT	---	---	A	E	295	Q
	* ID not provided by source

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

Asymmetric/Biological Unit (3, 3)

	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	1	A:108-119
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	PEPT1_DERPT	266-276	1	A:248-258
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	PEPT1_DERPT	283-302	1	A:265-284

(no "Exon" information available for 1XKG)

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:298
 aligned with PEPT1_DERPT | P08176 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:303
                                                                                                                                                                                                                                                                                                                                    320    
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311        |-   
          PEPT1_DERPT    22 SIKTFEEYKKAFNKSYATFEDEEAARKNFLESVKYVQSNGGAINHLSDLSLDEFKNRFLMSAEAFEHLKTQFDLNAETNACSINGNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNQSLDLAEQELVDCASQHGCHGDTIPRGIEYIQHNGVVQESYYRYVAREQSCRRPNAQRFGISNYCQIYPPNVNKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNYHAVNIVGYSNAQGVDYWIVRNSWDTNWGDNGYGYFAANIDLMMIEEYPYVVIL----   -
               SCOP domains d1xkga1 A:4-305 Major mite fecal allergen der p 1                                                                                                                                                                                                                                                             - SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------Peptidase_C1-1xkgA01 A:90-301                                                                                                                                                                                       ----- Pfam domains
         Sec.struct. author ...hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhh-----............ee.................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh........hhhhhhhhhhhhhee.hhhh...............ee...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
                 1xkg A   4 SIKTFEEYKKAFNKSYATFEDEEAARKNFLESVKYVQSNGGAINHLSDLSLDEFKNRFLMSAEAFEHLKTQFD-----NACSINGNAPAEIDLRQMRTVTPIRMQGGCGSAWAFSGVAATESAYLAYRDQSLDLAEQELVDCASQHGCHGDTIPRGIEYIQHNGVVQESYYRYVAREQSCRRPNAQRFGISNYCQIYPPNANKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNYHAVNIVGYSNAQGVDYWIVRNSWDTNWGDNGYGYFAANIDLMMIEEYPYVVILGQTG 306
                                    13        23        33        43        53        63        73  |     83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303   
                                                                                                   76    82

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)

d1xkga1

A:4-305

(no "CATH Domain" information available for 1XKG)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_CA (169)

Family: Peptidase_C1 (81)

Dermatophagoides pteronyssinus (European house dust mite) (1)

Peptidase_C1-1xkgA01

A:90-301

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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:200 - Pro A:201	[ RasMol ]

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

(no "Related Entries Specified in the PDB File" available for 1XKG)

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