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(-) Description

Title :  CRYSTAL STRUCTURE OF DER F 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 :  1.90
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Complex Between An Allergen And Fab Fragment Of 4C1 Antibody, 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 F 1 VARIANT
    Chains: A
    Fragment: UNP RESIDUES 99-321
    Organism Common: AMERICAN HOUSE DUST MITE
    Organism Scientific: DERMATOPHAGOIDES FARINAE
    Organism Taxid: 6954
 
Molecule 2 - 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 - 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, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:53binding site for residue NAG A 301
2AC2SOFTWAREASP A:57 , LEU A:58 , GLU A:60 , GLU A:92 , EDO A:304 , HOH A:421binding site for residue CA A 302
3AC3SOFTWAREALA A:50 , THR A:135 , HIS A:136binding site for residue EDO A 303
4AC4SOFTWAREARG A:27 , MET A:28 , ASP A:57 , GLU A:60 , GLU A:92 , CA A:302 , HOH A:437 , HOH A:553binding site for residue EDO A 304
5AC5SOFTWAREHOH A:409 , HOH A:442 , ASP C:92 , PHE C:94 , TYR C:96 , HOH C:450 , HOH C:471 , ARG D:103 , HOH D:357binding site for residue EDO C 301
6AC6SOFTWAREGLN C:37 , LYS C:39 , LYS C:45 , GLU C:81 , ASP C:82binding site for residue EDO C 302

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:118
2A:32 -A:72
3A:66 -A:104
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:121 -Pro A:122
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 5VPL)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VPL)

(-) 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:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee.................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhh.hhhhhhhhhhhhh..hhhhh....................eeee....hhhhhhhhhhhhh..eeeeeee.hhhhhhh...............eeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vpl A   1 TSACRINSVNVPSELDLRSLRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNTSLDLSEQELVDCASQHGCHGDTIPRGIEYIQQNGVVEERSYPYVAREQQCRRPNSQHYGISNYCQIYPPDVKQIREALTQTHTAIAVIIGIKDLRAFQHYDGRTIIQHDNGYQPNYHAVNIVGYGSTQGVDYWIVRNSWDTTWGDSGYGYFQAGNNLMMIEQYPYVVIM 223
                                    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..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vpl 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:216
                                                                                                                                                                                                                                                        
               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.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5vpl D   1 EVQLQESGPGLVKPSQSLSLTCTVTGYSITSDYAWNWIRQFPGNKLEWMGYISYSGTTSYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCGRTGVYRYPERAPYWGQGTLVTVSAAKTTPPSVYPLAPNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  146       156       166       176       186       196       206       216      
                                                                                                                                                               134|                                                                                 
                                                                                                                                                                141
   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 3RVV: 2,2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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
        I2CMD3_DERFA | I2CMD3: 5vpk
        Q7TS98_MOUSE | Q7TS98: 1d5b 1d5i 1d6v 2exp 2exq
UniProtKB/TrEMBL
        Q7TS98_MOUSE | Q7TS98: 1i8m 1jgl 1jhk 1jnl 1jnn 3bgf 3j42 4kvc

(-) Related Entries Specified in the PDB File

5vpg 5vph 5vpk