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(-) Description

Title :  CRYSTAL STRUCTURE OF DUST MITE ALLERGEN DER P 5
 
Authors :  G. A. Mueller, R. A. Gosavi, J. M. Krahn, L. L. Edwards, M. J. Cuneo, J. Gle A. Pomes, M. D. Chapman, R. E. London, L. C. Pedersen
Date :  27 Apr 10  (Deposition) - 02 Jun 10  (Release) - 24 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Biol. Unit 4:  E,F  (1x)
Keywords :  Allergen, Dust Mite (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. A. Mueller, R. A. Gosavi, J. M. Krahn, L. L. Edwards, M. J. Cuneo, J. Glesner, A. Pomes, M. D. Chapman, R. E. London, L. C. Pedersen
Der P 5 Crystal Structure Provides Insight Into The Group 5 Dust Mite Allergens.
J. Biol. Chem. V. 285 25394 2010
PubMed-ID: 20534590  |  Reference-DOI: 10.1074/JBC.M110.128306

(-) Compounds

Molecule 1 - MITE ALLERGEN DER P 5
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX4T3(TEV)
    Expression System StrainBL21(DE3)RIL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 34-132
    GeneDERP5
    Organism CommonEUROPEAN HOUSE DUST MITE
    Organism ScientificDERMATOPHAGOIDES PTERONYSSINUS
    Organism Taxid6956
    SynonymALLERGEN DER P V, IGE-BINDING ALLERGEN

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)
Biological Unit 2 (1x)AB    
Biological Unit 3 (1x)  CD  
Biological Unit 4 (1x)    EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 35)

Asymmetric Unit (3, 35)
No.NameCountTypeFull Name
1MPD17Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD17Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MPD-1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD-1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 19)
No.NameCountTypeFull Name
1MPD11Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD7Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 10)
No.NameCountTypeFull Name
1MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD4Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 4 (1, 6)
No.NameCountTypeFull Name
1MPD-1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD6Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
3PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:54 , LYS A:121 , LYS A:122 , MPD A:203 , LYS C:96BINDING SITE FOR RESIDUE MPD A 201
02AC2SOFTWAREGLY A:45 , ALA A:109 , SER A:112 , MPD A:209 , ILE B:38 , MRD B:204BINDING SITE FOR RESIDUE MRD A 202
03AC3SOFTWAREGLU A:54 , HIS A:58 , MPD A:201 , TYR D:51BINDING SITE FOR RESIDUE MPD A 203
04AC4SOFTWAREASP A:119 , LYS A:122 , GLU A:123 , ARG A:126 , HOH A:216 , LYS C:96BINDING SITE FOR RESIDUE MPD A 204
05AC5SOFTWAREARG A:118BINDING SITE FOR RESIDUE MRD A 207
06AC6SOFTWAREMPD C:212BINDING SITE FOR RESIDUE MPD A 208
07AC7SOFTWAREGLY A:45 , MET A:81 , MRD A:202 , ALA B:109 , MPD B:200 , MRD B:204 , MRD B:205BINDING SITE FOR RESIDUE MPD A 209
08AC8SOFTWAREASP A:69 , LYS A:70 , ALA A:73 , ASP B:97BINDING SITE FOR RESIDUE MPD A 210
09AC9SOFTWAREGLN A:53 , LEU A:120BINDING SITE FOR RESIDUE MPD A 200
10BC1SOFTWAREGLU A:102 , ASN A:105 , THR B:77 , MET B:81BINDING SITE FOR RESIDUE MRD A 133
11BC2SOFTWARETYR A:51 , LYS A:70 , ASP B:99 , PHE B:101BINDING SITE FOR RESIDUE MPD A 206
12BC3SOFTWAREGLU A:102 , ASN A:105 , ALA B:48 , GLU B:74BINDING SITE FOR RESIDUE MRD A 134
13BC4SOFTWAREILE A:78 , MET A:81 , MPD A:209 , GLU B:102 , ASN B:105BINDING SITE FOR RESIDUE MPD B 200
14BC5SOFTWAREGLN A:41 , MPD A:209 , ILE B:82 , ALA B:109BINDING SITE FOR RESIDUE MRD B 205
15BC6SOFTWAREVAL A:88 , ARG A:91 , GLY B:84 , VAL B:88 , ARG B:91 , HOH B:214BINDING SITE FOR RESIDUE PO4 B 213
16BC7SOFTWARELEU A:47 , PHE B:101 , ASN B:105 , PHE C:101BINDING SITE FOR RESIDUE MRD B 201
17BC8SOFTWAREGLY B:45 , MRD B:204BINDING SITE FOR RESIDUE MPD B 203
18BC9SOFTWAREMRD A:202 , MPD A:209 , MPD B:203BINDING SITE FOR RESIDUE MRD B 204
19CC1SOFTWARELEU B:98 , GLN B:103BINDING SITE FOR RESIDUE MPD B 133
20CC2SOFTWAREMPD A:208 , GLN C:103BINDING SITE FOR RESIDUE MPD C 212
21CC3SOFTWAREILE C:42 , SER C:112 , MRD C:203 , ILE D:38BINDING SITE FOR RESIDUE MPD C 200
22CC4SOFTWARELEU C:92 , GLU C:102 , LEU C:106BINDING SITE FOR RESIDUE MRD C 201
23CC5SOFTWAREHIS C:39BINDING SITE FOR RESIDUE MRD C 202
24CC6SOFTWAREILE C:42 , MPD C:200 , VAL D:85BINDING SITE FOR RESIDUE MRD C 203
25CC7SOFTWAREARG A:126 , LYS C:96BINDING SITE FOR RESIDUE MRD C 204
26CC8SOFTWAREALA C:48 , GLU C:74BINDING SITE FOR RESIDUE MPD C 208
27CC9SOFTWAREGLN C:53 , LEU C:120 , GLU C:123 , ASN D:32 , LEU D:34BINDING SITE FOR RESIDUE MPD D 206
28DC1SOFTWARELEU C:34 , MET C:35 , LEU D:52 , ILE D:56 , LEU D:120BINDING SITE FOR RESIDUE MPD D 207
29DC2SOFTWARETYR C:51 , ASN D:105 , PHE F:101BINDING SITE FOR RESIDUE MPD D 201
30DC3SOFTWARELEU E:106 , ALA E:109 , ALA F:48 , MRD F:200BINDING SITE FOR RESIDUE MRD E 200
31DC4SOFTWAREALA E:48 , GLN E:55 , GLU E:74 , LEU F:106 , MRD F:204BINDING SITE FOR RESIDUE MRD E 201
32DC5SOFTWAREGLY E:45 , ALA E:48 , LEU F:89BINDING SITE FOR RESIDUE MRD E 202
33DC6SOFTWARELEU E:47 , ALA E:48 , TYR E:51 , MRD E:201 , ASN F:105BINDING SITE FOR RESIDUE MRD F 204
34DC7SOFTWAREALA E:109 , MRD E:200 , GLY F:45BINDING SITE FOR RESIDUE MRD F 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MQ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MQ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 6)

Asymmetric Unit (1, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_ALL5_DERPT_001 *E61AALL5_DERPT  ---  ---A/B/C/D/E/FE61A
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_ALL5_DERPT_001 *E61AALL5_DERPT  ---  ---A/B/C/D/E/FE61A
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_ALL5_DERPT_001 *E61AALL5_DERPT  ---  ---A/BE61A
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_ALL5_DERPT_001 *E61AALL5_DERPT  ---  ---C/DE61A
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_ALL5_DERPT_001 *E61AALL5_DERPT  ---  ---E/FE61A
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MQ1)

(-) Exons   (0, 0)

(no "Exon" information available for 3MQ1)

(-) 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:101
 aligned with ALL5_DERPT | P14004 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:105
                                    37        47        57        67        77        87        97       107       117       127     
           ALL5_DERPT    28 NEFDFLLMERIHEQIKKGELALFYLQEQINHFEEKPTKEMKDKIVAEMDTIIAMIDGVRGVLDRLMQRKDLDIFEQYNLEMAKKSGDILERDLKKEEARVKKIEV 132
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------A----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3mq1 A  32 NS----LMERIHEQIKKGELALFYLQEQINHFEEKPTKEMKDKIVAEMDTIIAMIDGVRGVLDRLMQRKDLDIFEQYNLEMAKKSGDILERDLKKEEARVKKIEV 132
                             |    | 37        47        57        67        77        87        97       107       117       127     
                             |   34                                                                                                  
                            33                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:101
 aligned with ALL5_DERPT | P14004 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:105
                                    37        47        57        67        77        87        97       107       117       127     
           ALL5_DERPT    28 NEFDFLLMERIHEQIKKGELALFYLQEQINHFEEKPTKEMKDKIVAEMDTIIAMIDGVRGVLDRLMQRKDLDIFEQYNLEMAKKSGDILERDLKKEEARVKKIEV 132
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hh----hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------A----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3mq1 B  32 NS----LMERIHEQIKKGELALFYLQEQINHFEEKPTKEMKDKIVAEMDTIIAMIDGVRGVLDRLMQRKDLDIFEQYNLEMAKKSGDILERDLKKEEARVKKIEV 132
                             |    | 37        47        57        67        77        87        97       107       117       127     
                            33   34                                                                                                  

Chain C from PDB  Type:PROTEIN  Length:101
 aligned with ALL5_DERPT | P14004 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:105
                                    37        47        57        67        77        87        97       107       117       127     
           ALL5_DERPT    28 NEFDFLLMERIHEQIKKGELALFYLQEQINHFEEKPTKEMKDKIVAEMDTIIAMIDGVRGVLDRLMQRKDLDIFEQYNLEMAKKSGDILERDLKKEEARVKKIEV 132
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hh----hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------A----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3mq1 C  32 NS----LMERIHEQIKKGELALFYLQEQINHFEEKPTKEMKDKIVAEMDTIIAMIDGVRGVLDRLMQRKDLDIFEQYNLEMAKKSGDILERDLKKEEARVKKIEV 132
                             |    | 37        47        57        67        77        87        97       107       117       127     
                            33   34                                                                                                  

Chain D from PDB  Type:PROTEIN  Length:101
 aligned with ALL5_DERPT | P14004 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:105
                                    37        47        57        67        77        87        97       107       117       127     
           ALL5_DERPT    28 NEFDFLLMERIHEQIKKGELALFYLQEQINHFEEKPTKEMKDKIVAEMDTIIAMIDGVRGVLDRLMQRKDLDIFEQYNLEMAKKSGDILERDLKKEEARVKKIEV 132
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hh----hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------A----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3mq1 D  32 NS----LMERIHEQIKKGELALFYLQEQINHFEEKPTKEMKDKIVAEMDTIIAMIDGVRGVLDRLMQRKDLDIFEQYNLEMAKKSGDILERDLKKEEARVKKIEV 132
                             |    | 37        47        57        67        77        87        97       107       117       127     
                            33   34                                                                                                  

Chain E from PDB  Type:PROTEIN  Length:100
 aligned with ALL5_DERPT | P14004 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:104
                                    37        47        57        67        77        87        97       107       117       127    
           ALL5_DERPT    28 NEFDFLLMERIHEQIKKGELALFYLQEQINHFEEKPTKEMKDKIVAEMDTIIAMIDGVRGVLDRLMQRKDLDIFEQYNLEMAKKSGDILERDLKKEEARVKKIE 131
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hh----hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------A---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3mq1 E  32 NS----LMERIHEQIKKGELALFYLQEQINHFEEKPTKEMKDKIVAEMDTIIAMIDGVRGVLDRLMQRKDLDIFEQYNLEMAKKSGDILERDLKKEEARVKKIE 131
                             |    | 37        47        57        67        77        87        97       107       117       127    
                            33   34                                                                                                 

Chain F from PDB  Type:PROTEIN  Length:100
 aligned with ALL5_DERPT | P14004 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:100
                                    42        52        62        72        82        92       102       112       122       132
           ALL5_DERPT    33 LLMERIHEQIKKGELALFYLQEQINHFEEKPTKEMKDKIVAEMDTIIAMIDGVRGVLDRLMQRKDLDIFEQYNLEMAKKSGDILERDLKKEEARVKKIEV 132
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Blo-t-5-3mq1F01 F:34-132                                                                            Pfam domains (1)
           Pfam domains (2) -Blo-t-5-3mq1F02 F:34-132                                                                            Pfam domains (2)
           Pfam domains (3) -Blo-t-5-3mq1F03 F:34-132                                                                            Pfam domains (3)
           Pfam domains (4) -Blo-t-5-3mq1F04 F:34-132                                                                            Pfam domains (4)
           Pfam domains (5) -Blo-t-5-3mq1F05 F:34-132                                                                            Pfam domains (5)
           Pfam domains (6) -Blo-t-5-3mq1F06 F:34-132                                                                            Pfam domains (6)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------A----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3mq1 F  33 SLMERIHEQIKKGELALFYLQEQINHFEEKPTKEMKDKIVAEMDTIIAMIDGVRGVLDRLMQRKDLDIFEQYNLEMAKKSGDILERDLKKEEARVKKIEV 132
                                    42        52        62        72        82        92       102       112       122       132

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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)

(no "SCOP Domain" information available for 3MQ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MQ1)

(-) Pfam Domains  (1, 6)

Asymmetric Unit

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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3MQ1)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3MQ1)