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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 :  1.95
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  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 - DER P 1 ALLERGEN
    Chains: A
    Fragment: UNP RESIDUES 99-320
    Organism Common: EUROPEAN HOUSE DUST MITE
    Organism Scientific: DERMATOPHAGOIDES PTERONYSSINUS
    Organism Taxid: 6956
 
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  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2EDO8Ligand/Ion1,2-ETHANEDIOL
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:56 , LEU A:57 , GLU A:59 , GLU A:91 , EDO A:302 , HOH A:430binding site for residue CA A 301
02AC2SOFTWAREARG A:26 , MET A:27 , ASP A:56 , GLU A:59 , GLU A:91 , CA A:301 , HOH A:411binding site for residue EDO A 302
03AC3SOFTWARETHR A:21 , ALA A:49 , HIS A:135 , GLY A:182 , VAL A:183 , ASP A:184 , HOH A:514binding site for residue EDO A 303
04AC4SOFTWARETHR A:1 , ALA A:3 , GLN A:118 , TYR A:120binding site for residue EDO A 304
05AC5SOFTWAREGLN A:109 , LYS A:145 , GLY A:164 , TYR A:165 , GLN A:166 , HOH A:526binding site for residue EDO A 305
06AC6SOFTWARETHR A:23 , PRO A:24 , ARG A:26 , SER A:54 , LEU A:55 , ASP A:56 , HOH A:539binding site for residue EDO A 306
07AC7SOFTWAREGLN C:37 , LYS C:39 , LYS C:45 , PHE C:62 , GLU C:81 , ASP C:82binding site for residue EDO C 301
08AC8SOFTWAREASN A:199 , TYR C:96 , EDO C:303 , HOH C:413 , HOH C:416 , HOH D:321binding site for residue EDO C 302
09AC9SOFTWARETYR C:91 , TYR C:96 , EDO C:302 , GLY D:100 , TYR D:102binding site for residue EDO C 303
10AD1SOFTWAREASN A:52 , ASN A:125 , HOH A:464binding site for Mono-Saccharide NAG A 307 bound to ASN A 52

(-) 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 5VPG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VPG)

(-) 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 .............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
                 5vpg 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......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vpg 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:218
                                                                                                                                                                                                                                                          
               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.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vpg D   1 EVQLQESGPGLVKPSQSLSLTCTVTGYSITSDYAWNWIRQFPGNKLEWMGYISYSGTTSYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCGRTGVYRYPERAPYWGQGTLVTVSAAKTTPPSVYPLAPQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  144       154       164       174       184       194       204       214        
                                                                                                                                                               134|                                                                                   
                                                                                                                                                                139
   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  (0, 0 ; only for superseded entry 3RVW: 2,2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q3HWZ5_DERPT | Q3HWZ5: 5vcn 5vco
UniProtKB/TrEMBL
        Q3HWZ5_DERPT | Q3HWZ5: 3f5v

(-) Related Entries Specified in the PDB File

3rvt 3rvu 3rvv 3rvx 5vph 5vpk 5vpl