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(-) Description

Title :  CRYSTAL STRUCTURE OF MITE ALLERGEN DER F 1
 
Authors :  M. Chruszcz, M. D. Chapman, L. D. Vailes, A. Pomes, W. Minor
Date :  05 May 17  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Allergy, Dust Mites, Allergen, Glycoprotein, Hydrolase, Protease, Secreted, Thiol Protease, Zymogen (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 F 1 VARIANT
    Chains: A, B, C
    Fragment: SEQUENCE DATABASE RESIDUES 99-321
    Organism Common: AMERICAN HOUSE DUST MITE
    Organism Scientific: DERMATOPHAGOIDES FARINAE
    Organism Taxid: 6954

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO45Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:102 , GLN A:103binding site for residue SO4 A 301
2AC2SOFTWAREASN A:53 , THR A:54 , SER A:55binding site for residue SO4 A 302
3AC3SOFTWARETYR A:204binding site for residue SO4 A 304
4AC4SOFTWARETHR A:76 , PRO A:78 , HOH A:439 , ARG B:79binding site for residue SO4 A 305
5AC5SOFTWAREALA A:131 , GLN A:134 , THR A:135 , VAL A:220binding site for residue SO4 A 306
6AC6SOFTWAREARG B:5 , ILE B:6 , GLN B:134 , THR B:135binding site for residue SO4 B 302
7AC7SOFTWAREGLY A:31 , ASN A:53 , GLN B:167binding site for Mono-Saccharide NAG A 303 bound to ASN A 53
8AC8SOFTWAREGLN A:167 , PRO A:168 , GLY B:31 , ASN B:53binding site for Mono-Saccharide NAG B 301 bound to ASN B 53

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:4 -A:118
2A:32 -A:72
3A:66 -A:104
4B:4 -B:118
5B:32 -B:72
6B:66 -B:104
7C:4 -C:118
8C:32 -C:72
9C:66 -C:104

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Tyr A:121 -Pro A:122
2Tyr B:121 -Pro B:122
3Tyr C:121 -Pro C:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VPK)

(-) 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:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eehhhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh........hhhhhhhhhhhhh..hhhhh....................eeee....hhhhhhhhhhhhh..eeeeeee.hhhhhhh...............eeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vpk 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 B from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eehhhhh............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
                 5vpk B   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:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eehhhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh........hhhhhhhhhhhhh..hhhhh....................eeee....hhhhhhhhhhhhh..eeeeeee.hhhhhhh...............eeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vpk C   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
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5VPK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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 Related Entries

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UniProtKB/Swiss-Prot
        I2CMD3_DERFA | I2CMD3: 5vpl

(-) Related Entries Specified in the PDB File

5vpg 5vph 5vpl