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

(-) Description

Title :  STRUCTURE OF A PLASMODIUM FALCIPARUM APICAL MEMBRANE ANTIGEN 1-FAB F8.12.19 COMPLEX
 
Authors :  S. Igonet, B. Vulliez-Le Normand, G. Faure, M. M. Riottot, C. H. M. Kocken, A. W. Thomas, G. A. Bentley
Date :  18 Sep 06  (Deposition) - 30 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Malaria Vaccine Candidate, Apical Membrane Antigen 1, Hypothetical Protein, Immunoglobulin Domain, Membrane, Merozoite, Transmembrane, Immune System, Immunoglobulin C Region, Antibody Cross-Reactivity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Igonet, B. Vulliez-Le Normand, G. Faure, M. M. Riottot, C. H. M. Kocken, A. W. Thomas, G. A. Bentley
Cross-Reactivity Studies Of An Anti-Plasmodium Vivax Apical Membrane Antigen 1 Monoclonal Antibody: Binding And Structural Characterisation.
J. Mol. Biol. V. 366 1523 2007
PubMed-ID: 17229439  |  Reference-DOI: 10.1016/J.JMB.2006.12.028

(-) Compounds

Molecule 1 - APICAL MEMBRANE ANTIGEN 1
    Chains: A
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPICZALPHAA
    Expression System Taxid: 4922
    Fragment: PFAMA1 ECTOPLASMIC REGION, RESIDUES 25-605
    Mutation: YES
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833
    Strain: FVO
    Synonym: PLASMODIUM FALCIPARUM APICAL MEMBRANE ANTIGEN 1
 
Molecule 2 - FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19
    Chains: B
    Fragment: ANTIGEN-BINDING FRAGMENT FAB, LIGHT CHAIN
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: MONOCLONAL ANTIBODY ISOTYPE IS IGG1, KAPPA
    Strain: BALB/C
 
Molecule 3 - FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19
    Chains: C
    Fragment: ANTIGEN-BINDING FRAGMENT FAB, HEAVY CHAIN
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: MONOCLONAL ANTIBODY ISOTYPE IS IGG1, KAPPA.
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 2J5L)

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:490 -A:507
2A:492 -A:509
3B:23 -B:88
4B:134 -B:194
5B:214 -C:233
6C:22 -C:92
7C:142 -C:208

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser B:7 -Pro B:8
2His B:94 -Pro B:95
3Tyr B:140 -Pro B:141
4Phe C:148 -Pro C:149
5Glu C:150 -Pro C:151
6Arg C:199 -Pro C:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J5L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J5L)

(-) Exons   (0, 0)

(no "Exon" information available for 2J5L)

(-) 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:34
 aligned with Q9BIM8_PLAFA | Q9BIM8 from UniProtKB/TrEMBL  Length:402

    Alignment length:34
                                   352       362       372    
        Q9BIM8_PLAFA    343 IFISDDKDSLKCPCDPEMVSNSTCRFFVCKCVER  376
               SCOP domains d2j5la1 A:479-512                  SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhh.....ee........ee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                2j5l A  479 IFISDDKDSLKCPCDPEMVSQSTCRFFVCKCVER  512
                                   488       498       508    


Chain A from PDB  Type:PROTEIN  Length:34
 aligned with Q9GVB7_PLAFA | Q9GVB7 from UniProtKB/TrEMBL  Length:605

    Alignment length:34
                                   480       490       500    
        Q9GVB7_PLAFA    471 IFISDDKDSLKCPCDPEMVSNSTCRFFVCKCVER  504
               SCOP domains d2j5la1 A:479-512                  SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author ..ee..hhhhh.....ee........ee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                2j5l A  479 IFISDDKDSLKCPCDPEMVSQSTCRFFVCKCVER  512
                                   488       498       508    


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with Q5XFY8_MOUSE | Q5XFY8 from UniProtKB/TrEMBL  Length:235

    Alignment length:221
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234 
        Q5XFY8_MOUSE     15 ASVIMSRGQIVLSQSPAILSGFPGEKVTMTCRASSSVNYMHWYQQKPGSSPKPWIYATSKLASGVPARFSGSGSGTSYSLTISRVEAEDAATYYCQQWSSNPLTFGAGTRLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  235
               SCOP domains d2        j5lb1 B:1-107 automated matches                                                                         d2j5lb2 B:108-214 automated matches                                                                         SCOP domains
               CATH domains -2        j5lB01 B:2-108 Immunoglobulins                                                                           2j5lB02 B:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..--------.eeee..eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee......eeeee...ee...eeeee.........eeeeeeeeeehhhhhh..eeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2j5l B    1 xS--------VLSQSPAILSASPGEKVTMTCRARSSVSYMHWYQQKSGSSPKPWIHATSNLASGVPARFSGSGSGTSYSLTISRVEAEDAATYYCQQWSSHPPTFGSGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                            ||       -|       12        22    ||  33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213 
                            ||        3                      27|                                                                                                                                                                                         
                            1-PCA                             29                                                                                                                                                                                         
                             2                                                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                  
               SCOP domains d2j5lc1 C:1-112 Immunoglobulin heavy chain variable domain, VH                                                            d2j5lc2 C:113-233 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 2j5lC01 C:1-113 Immunoglobulins                                                                                            2j5lC02 C:114-227 Immunoglobulins                                                                  --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhh...eeeee.....eeeeee...hhhhheeeeeee..hhhhh......ee...eeeee........eeeee..........eeeeeeeee.......eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2j5l C    1 EVQLVESGGGLVKPGGSLKLSCAASGFIFSDYYMYWVRQTPEKRLEWVATISDGNSYTYYVDSVKGRFTISRDNAKNNLYLQMSSLKSEDTAIYYCARDGPTDSSGYGGFGYWGQGTLVTVSEAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC  233
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F       110       120       130|      142       152 ||||  167 ||    178 ||    190     ||202   ||  213       223| || 
                                                                              52A                            82A||               100A|||||                           130|                  154|||    169|      180|          196| || 206|            223| || 
                                                                                                              82B|                100B||||                            133                   156||     171       183           198 ||  208             226 || 
                                                                                                               82C                 100C|||                                                   157|                               200|                    228| 
                                                                                                                                    100D||                                                    162                                202                     232 
                                                                                                                                     100E|                                                                                                                   
                                                                                                                                      100F
   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  (5, 5)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J5L)

(-) Gene Ontology  (3, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9BIM8_PLAFA | Q9BIM8)
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A   (Q9GVB7_PLAFA | Q9GVB7)
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B   (Q5XFY8_MOUSE | Q5XFY8)

 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
    PCA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2j5l)
 
  Cis Peptide Bonds
    Arg C:199 - Pro C:200   [ RasMol ]  
    Glu C:150 - Pro C:151   [ RasMol ]  
    His B:94 - Pro B:95   [ RasMol ]  
    Phe C:148 - Pro C:149   [ RasMol ]  
    Ser B:7 - Pro B:8   [ RasMol ]  
    Tyr B:140 - Pro B:141   [ 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
  2j5l
    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
  Q5XFY8_MOUSE | Q5XFY8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q9BIM8_PLAFA | Q9BIM8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q9GVB7_PLAFA | Q9GVB7
    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
  Q5XFY8_MOUSE | Q5XFY8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9BIM8_PLAFA | Q9BIM8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9GVB7_PLAFA | Q9GVB7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5XFY8_MOUSE | Q5XFY8: 2j4w 3oz9
        Q9BIM8_PLAFA | Q9BIM8: 2mtx

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2J5L)