Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-MSP2 FV FRAGMENT (MAB6D8)IN COMPLEX WITH FC27-MSP2 14-30
 
Authors :  R. A. V. Morales, C. A. Macraild, J. Seow, K. Bankala, N. Drinkwater, S. M R. Rouet, D. Christ, R. F. Anders, R. S. Norton
Date :  22 Jul 14  (Deposition) - 03 Jun 15  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym./Biol. Unit :  A,B,Q
Keywords :  Immunoglobulin Fold, Immune System, N-Terminal Msp2, Unstructured Antigen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. A. Morales, C. A. Macraild, J. Seow, B. Krishnarjuna, N. Drinkwater R. Rouet, R. F. Anders, D. Christ, S. Mcgowan, R. S. Norton
Structural Basis For Epitope Masking And Strain Specificity Of A Conserved Epitope In An Intrinsically Disordered Malaria Vaccine Candidate.
Sci Rep V. 5 10103 2015
PubMed-ID: 25965408  |  Reference-DOI: 10.1038/SREP10103

(-) Compounds

Molecule 1 - FV FRAGMENT(MAB6D8) HEAVY CHAIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - FV FRAGMENT(MAB6D8) LIGHT CHAIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - MEROZOITE SURFACE ANTIGEN 2
    Chains: Q
    Engineered: YES
    Fragment: UNP RESIDUES 33-49
    Organism Scientific: PLASMODIUM FALCIPARUM K1
    Organism Taxid: 5839
    Synonym: MEROZOITE SURFACE PROTEIN 2, MSA-2
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABQ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP

(-) Sites  (0, 0)

(no "Site" information available for 4QXT)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:96
2B:23 -B:92

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser B:7 -Pro B:8
2His B:80 -Pro B:81
3Asp B:98 -Pro B:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QXT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QXT)

(-) Exons   (0, 0)

(no "Exon" information available for 4QXT)

(-) 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:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee....ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4qxt A   1 QVQLQQSGDELVKPGASVKLSCTVSGFNIKDDFIHWMKQRPEQGLEWIGRIDPANGYTKYAPKFQDKATMTADTSSNTAYLQLSSLASEDAAVYYCATYGVAYWGQGTLVTVSA 114
                                    10        20        30        40        50        60        70        80        90       100       110    


Chain B from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4qxt B   1 DIVLTQSPASLAVSLGQRATISCKASQSVDHDGDSYMNWFQQKPGQSPKLLIYAASNLESGIPARFSGSGSGTDFTLNIHPVEEEDAATYYCQQTNEDPYTFGGGTKLEIK 111
                                    10        20        30        40        50        60        70        80        90       100       110 


Chain Q from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4qxt Q  13 xNAYNMSIRRS  23
                            |       22 
                           13-ACE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4QXT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QXT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QXT)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4qxt)
 
  Cis Peptide Bonds
    Asp B:98 - Pro B:99   [ RasMol ]  
    His B:80 - Pro B:81   [ RasMol ]  
    Ser B:7 - Pro B:8   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4qxt
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MSA2_PLAFK | Q03643
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MSA2_PLAFK | Q03643
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MSA2_PLAFK | Q03643: 4qyo

(-) Related Entries Specified in the PDB File

4qy8 THE SAME FV FRAGMENT COMPLEXED WITH 3D7-MSP2 14-30
4qyo ANTI-MSP2 FV FRAGMENT (MAB6D8)IN COMPLEX WITH MSP2 14-22