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(-) Description

Title :  CRYSTAL STRUCTURE OF DER P 1 COMPLEXED WITH FAB 4C1
 
Authors :  M. Chruszcz, L. D. Vailes, M. D. Chapman, A. Pomes, W. Minor
Date :  05 May 17  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Der P 1, Allergen-Antibody Complex, Hydrolase-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Chruszcz, A. Pomes, J. Glesner, L. D. Vailes, T. Osinski, P. J. Porebski, K. A. Majorek, P. W. Heymann, T. A. Platts-Mills, W. Minor, M. D. Chapman
Molecular Determinants For Antibody Binding On Group 1 Hous Dust Mite Allergens.
J. Biol. Chem. V. 287 7388 2012
PubMed-ID: 22210776  |  Reference-DOI: 10.1074/JBC.M111.311159

(-) Compounds

Molecule 1 - PEPTIDASE 1
    Chains: A
    EC Number: 3.4.22.65
    Fragment: UNP RESIDUES 99-320
    Organism Common: EUROPEAN HOUSE DUST MITE
    Organism Scientific: DERMATOPHAGOIDES PTERONYSSINUS
    Organism Taxid: 6956
    Synonym: ALLERGEN DER P I, MAJOR MITE FECAL ALLERGEN DER P 1
 
Molecule 2 - FAB 4C1 - LIGHT CHAIN
    Chains: C
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA
    Expression System Taxid: 10090
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - FAB 4C1 - HEAVY CHAIN
    Chains: D
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA
    Expression System Taxid: 10090
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (0, 0)

(no "Site" information available for 5VPH)

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:117
2A:31 -A:71
3A:65 -A:103
4C:23 -C:88
5C:134 -C:194
6D:22 -D:96
7D:148 -D:203

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Tyr A:120 -Pro A:121
2Ser C:7 -Pro C:8
3Phe C:94 -Pro C:95
4Tyr C:140 -Pro C:141
5Tyr D:104 -Pro D:105
6Phe D:154 -Pro D:155
7Glu D:156 -Pro D:157
8Trp D:196 -Pro D:197

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5VPH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5VPH)

(-) Exons   (0, 0)

(no "Exon" information available for 5VPH)

(-) Sequences/Alignments

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
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee..........eehhhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhh.hhhhhhhhhhhhhee.hhhh...............ee...eeee....hhhhhhhhhhhhh..eeeeeee.hhhhhhh.....ee........eeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5vph A   1 TNACSINGNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNQSLDLAEQELVDCASQHGCHGDTIPRGIEYIQHNGVVQESYYRYVAREQSCRRPNAQRFGISNYCQIYPPNANKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNYHAVNIVGYSNAQGVDYWIVRNSWDTNWGDNGYGYFAANIDLMMIEEYPYVVIL 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  


Chain C from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vph C   1 QIVMTQSPFSMYATLGERVTITCKASQDIYSYLSWLQQKPGKSLKTLIYRANRLITGVPSRFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPYTFGGGTKLEMKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 


Chain D from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeee.....eeeeeeee....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee..........ee...eeeee........eeeee....eeeeeeeeeee.....eeee.........ee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vph D   1 EVQLQESGPGLVKPSQSLSLTCTVTGYSITSDYAWNWIRQFPGNKLEWMGYISYSGTTSYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCGRTGVYRYPERAPYWGQGTLVTVSAAKTTPPSVYPLAPGSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 146       156       166       176       186       196       206       216    
                                                                                                                                                                135|                                                                              
                                                                                                                                                                 142
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0 ; only for superseded entry 3RVX: 2,2)

(no "SCOP Domain" information available for 5VPH, only for superseded entry 3RVX replaced by 5VPH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5VPH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5VPH)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu D:156 - Pro D:157   [ RasMol ]  
    Phe C:94 - Pro C:95   [ RasMol ]  
    Phe D:154 - Pro D:155   [ RasMol ]  
    Ser C:7 - Pro C:8   [ RasMol ]  
    Trp D:196 - Pro D:197   [ RasMol ]  
    Tyr A:120 - Pro A:121   [ RasMol ]  
    Tyr C:140 - Pro C:141   [ RasMol ]  
    Tyr D:104 - Pro D:105   [ RasMol ]  
 

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  5vph
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  PEPT1_DERPT | P08176
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  3.4.22.65
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PEPT1_DERPT | P08176: 1xkg 2as8 3rvw 3rvx 4pp1 4pp2

(-) Related Entries Specified in the PDB File

3rvt 3rvu 3rvv 3rvw 5vpg 5vpk 5vpl