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(-) Description

Title :  C2 CRYSTAL FORM OF MITE ALLERGEN DER P 1
 
Authors :  E. A. Stura, W. Minor, M. Chruszcz, J. M. Saint Remy
Date :  04 Nov 08  (Deposition) - 10 Feb 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.36
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Allergy, Asthma, Dust Mites, Allergen, Glycoprotein, Hydrolase, Protease, Secreted, Thiol Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Chruszcz, M. D. Chapman, L. D. Vailes, E. A. Stura, J. M. Saint-Remy, W. Minor, A. Pomes
Crystal Structures Of Mite Allergens Der F 1 And Der P 1 Reveal Differences In Surface-Exposed Residues That May Influence Antibody Binding.
J. Mol. Biol. V. 386 520 2009
PubMed-ID: 19136006  |  Reference-DOI: 10.1016/J.JMB.2008.12.049

(-) Compounds

Molecule 1 - DER P 1 ALLERGEN
    Chains: A, B
    EC Number: 3.4.22.65
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PCR4-BLUNT
    Expression System Strain: X-33
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Gene: DERP1
    Mutation: YES
    Organism Common: HOUSE-DUST MITE
    Organism Scientific: DERMATOPHAGOIDES PTERONYSSINUS
    Organism Taxid: 6956

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CSD2Mod. Amino Acid3-SULFINOALANINE
3P6G5Ligand/IonHEXAETHYLENE GLYCOL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CSD1Mod. Amino Acid3-SULFINOALANINE
3P6G2Ligand/IonHEXAETHYLENE GLYCOL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CSD1Mod. Amino Acid3-SULFINOALANINE
3P6G3Ligand/IonHEXAETHYLENE GLYCOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:56 , LEU A:57 , GLU A:59 , GLU A:91 , HOH A:248 , HOH A:321BINDING SITE FOR RESIDUE CA A 223
2AC2SOFTWARETYR A:169 , TYR A:216 , HOH A:661 , HOH A:668 , HOH B:697 , HOH B:727BINDING SITE FOR RESIDUE P6G A 224
3AC3SOFTWAREGLY A:29 , ARG A:151 , HOH A:333 , HOH B:544BINDING SITE FOR RESIDUE P6G A 225
4AC4SOFTWAREASP B:56 , LEU B:57 , GLU B:59 , GLU B:91 , HOH B:269 , HOH B:313BINDING SITE FOR RESIDUE CA B 223
5AC5SOFTWAREARG B:156 , GLN B:181 , TYR B:185 , HOH B:580BINDING SITE FOR RESIDUE P6G B 224
6AC6SOFTWAREGLN B:53 , LEU B:55 , GLN B:90 , GLN B:109 , PHE B:111BINDING SITE FOR RESIDUE P6G B 225
7AC7SOFTWARETYR B:216 , HOH B:721BINDING SITE FOR RESIDUE P6G B 226

(-) SS Bonds  (6, 6)

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

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F5V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F5V)

(-) Exons   (0, 0)

(no "Exon" information available for 3F5V)

(-) Sequences/Alignments

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:222
 aligned with Q3HWZ5_DERPT | Q3HWZ5 from UniProtKB/TrEMBL  Length:302

    Alignment length:222
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  
         Q3HWZ5_DERPT    81 TNACSINGNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNQSLDLAEQELVDCASQHGCHGDTIPRGIEYIQHNGVVQESYYRYVAREQSCRRPNAQRFGISNYCQIYPPNANKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNYHAVNIVGYSNAQGVDYWIVRNSWDTNWGDNGYGYFAANIDLMMIEEYPYVVIL 302
               SCOP domains d3f5va_ A: Major mite fecal allergen der p 1                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eehhhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh........hhhhhhhhhhhhhee.hhhh...............ee...eeee....hhhhhhhhhhhhh..eeeeeee.hhhhhhh...............eeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3f5v 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  
                                                            34-CSD                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:222
 aligned with Q3HWZ5_DERPT | Q3HWZ5 from UniProtKB/TrEMBL  Length:302

    Alignment length:222
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  
         Q3HWZ5_DERPT    81 TNACSINGNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNQSLDLAEQELVDCASQHGCHGDTIPRGIEYIQHNGVVQESYYRYVAREQSCRRPNAQRFGISNYCQIYPPNANKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNYHAVNIVGYSNAQGVDYWIVRNSWDTNWGDNGYGYFAANIDLMMIEEYPYVVIL 302
               SCOP domains d3f5vb_ B: Major mite fecal allergen der p 1                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eehhhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh........hhhhhhhhhhhhhee.hhhh...............ee...eeee....hhhhhhhhhhhhh..eeeeeee.hhhhhhh...............eeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3f5v 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  
                                                            34-CSD
   Legend:   → Mismatch (orange background)
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F5V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F5V)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q3HWZ5_DERPT | Q3HWZ5)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.

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 Related Entries

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        Q3HWZ5_DERPT | Q3HWZ5: 5vcn 5vco 5vpg

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