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(-) Description

Title :  CRYSTAL STRUCTURE OF DBP IN COMPLEX WITH INHIBITORY MONOCLONAL ANTIBODY 2D10
 
Authors :  E. Chen, N. D. Salinas, N. H. Tolia
Date :  02 Dec 15  (Deposition) - 18 May 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Plasmodium, Vivax, Duffy Binding Protein, Dbp, Antibody, Malaria, Scfv, Neutralizing, Interaction, Immune, Blocking, Invasion, Vaccine, Therapeutic, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Chen, N. D. Salinas, Y. Huang, F. Ntumngia, M. D. Plasencia, M. L. Gross, J. H. Adams, N. H. Tolia
Broadly Neutralizing Epitopes In The Plasmodium Vivax Vaccine Candidate Duffy Binding Protein.
Proc. Natl. Acad. Sci. Usa V. 113 6277 2016
PubMed-ID: 27194724  |  Reference-DOI: 10.1073/PNAS.1600488113

(-) Compounds

Molecule 1 - DUFFY RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 211-525
    Gene: PVDR
    Organism Scientific: PLASMODIUM VIVAX (STRAIN SALVADOR I)
    Organism Taxid: 126793
    Strain: SALVADOR I
    Synonym: ERYTHROCYTE-BINDING PROTEIN
 
Molecule 2 - ANTIBODY 2D10 SINGLE CHAIN VARIABLE FRAGMENT
    Chains: C, D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5F3J)

(-) Sites  (0, 0)

(no "Site" information available for 5F3J)

(-) SS Bonds  (11, 11)

Asymmetric Unit
No.Residues
1A:230 -A:237
2A:415 -A:432
3A:427 -A:507
4A:436 -A:505
5B:230 -B:237
6B:415 -B:432
7B:427 -B:507
8C:62 -C:132
9C:191 -C:265
10D:62 -D:132
11D:191 -D:265

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr C:138 -Pro C:139
2Tyr D:138 -Pro D:139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F3J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F3J)

(-) Exons   (0, 0)

(no "Exon" information available for 5F3J)

(-) 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:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhh...hhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f3j A 219 YKRKRRERDWDCNTKKDVCIPDRRYQLCMKELTNFRKLYLKRKLIYDAAVEGDLLLKLNNYRYNKDFCKDIRWSLGDFGDIIMGTDMEGIGYSKVVENNLRSIFGTDEKAQQRRKQWWNESKAQIWTAMMEPQIYRWIREWGRDYVSELPTEVQKLKEKCDGKITDKKVCKVPPCQNACKSYDQWITRKKNQWDVLSNKFISVKNAEKVQTAGIVTPYDILKQELDEFNEVAFENEINKRDGAYIELCVCS 508
                                   228       238       248   ||  272       282       292       302       312       322       332       342       352       362|      395       405       415   ||  427       437       447       457       467       477       487       497       507 
                                                           252|                                                                                            362|                              419|                                                                                      
                                                            267                                                                                             386                               422                                                                                      


Chain B from PDB  Type:PROTEIN  Length:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh...hhhhhhhhhh....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f3j B 219 YKRKRRERDWDCNTKKDVCIPDRRYQLCMKELTNLFRKLYLKRKLIYDAAVEGDLLLKLNNYRYNKDFCKDIRWSLGDFGDIIMEGIGYSKVVENNLRSIFGTDEKAQQRRKQWWNESKAQIWTAMMYSVKPQIYRWIREWGRDYVSELPTEVQKLKEKCDGKIYTDKKVCKVPPCQNACKSYDQWITRKKNQWDVLSNKFISVKNAEKVGIVTPYDILKQELDEFNEVAFENEINKRDGAYIELCVCS 508
                                   228       238       248    || 271       281       291       301       311   ||  325       335       345       355       365||     395       405       415   ||  426       436       446       456       466|      479       489       499         
                                                            253|                                             315|                                           366|                             419|                                          466|                                      
                                                             267                                              320                                            387                              421                                           470                                      


Chain C from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee...............eeee............eeeeee.....eeeeee............ee......eee.ee.........eeeeee...................eee...ee.......eeeeee.hhhhh.eeeeeeee.....eeeeeeee....eeee.......eeeeee....eeeeee...hhhhh.eeeeeeee.....eeee...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f3j C  40 DIVITQDELSNPVTSGESVSISCRSSKSLLYQDGKTYLNWFLQRPGQSPQLLIYLMSTRASGVSDRFSGSGSGTDFTLEISRVEAEDVGVYYCQQLVEYPLTFGAGTKLELKRQLQQSGPELVKPGASVKISCKASGYAFISSWMNWVKQRPGKGLEWIGRIYPGDGDTHYNGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCAREETATGGFDYWGQGTTLTV 287
                                    49        59        69        79        89        99       109       119       129       139       149  ||   178       188       198       208       218       228       238       248       258       268  ||   279        
                                                                                                                                          152|                                                                                                271|              
                                                                                                                                           172                                                                                                 273              


Chain D from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee...............eeee............eeeeee.....eeeee.............ee......eee.ee.........eeeeee......ee...........eee...ee......eeeeeee.hhhhh.eeeeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhh.eeeeeeee......eeee...eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f3j D  40 DIVITQDELSNPVTSGESVSISCRSSKSLLYQDGKTYLNWFLQRPGQSPQLLIYLMSTRASGVSDRFSGSGSGTDFTLEISRVEAEDVGVYYCQQLVEYPLTFGAGTKLELKRQLQQSGPELVKPGASVKISCKASGYAFISSWMNWVKQRPGKGLEWIGRIYPGDGDTHYNGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCAREETAQTGGFDYWGQGTTLT 286
                                    49        59        69        79        89        99       109       119       129       139       149  ||   178       188       198       208       218       228       238       248       258       268       278        
                                                                                                                                          152|                                                                                                                  
                                                                                                                                           172
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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 5F3J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F3J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F3J)

(-) Gene Ontology  (4, 4)

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  Cis Peptide Bonds
    Tyr C:138 - Pro C:139   [ RasMol ]  
    Tyr D:138 - Pro D:139   [ RasMol ]  
 
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        PVDR_PLAVS | P22290: 3rrc 4nuu 4nuv 4yfs

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