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

(-) Description

Title :  STRUCTURAL BASE OF THE INTERACTION OF A MONOCLONAL ANTIBODY AGAINST P24 OF HIV-1 WITH ITS PEPTIDE EPITOPE
 
Authors :  W. E. Hoehne, R. -D. Stigler
Date :  27 Dec 93  (Deposition) - 26 Jan 95  (Release) - 01 Apr 03  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  H,L,P
Keywords :  Complex(Immunoglobulin/Peptide) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. E. Hohne, G. Kuttner, S. Kiessig, G. Hausdorf, R. Grunow, K. Winkler, H. Wessner, E. Giessmann, R. Stigler, J. Schneider-Mergener, Et Al.
Structural Base Of The Interaction Of A Monoclonal Antibody Against P24 Of Hiv-1 With Its Peptide Epitope.
Mol. Immunol. V. 30 1213 1993
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGG2A CB 4-1 FV (LIGHT CHAIN)
    Chains: L
    Engineered: YES
    Organism Scientific: MUS MUSCULUS
 
Molecule 2 - IGG2A CB 4-1 FV (HEAVY CHAIN)
    Chains: H
    Engineered: YES
    Organism Scientific: MUS MUSCULUS
 
Molecule 3 - 
    Chains: P
    Engineered: YES

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1IIF)

(-) Sites  (0, 0)

(no "Site" information available for 1IIF)

(-) SS Bonds  (2, 2)

Theoretical Model
No.Residues
1H:22 -H:96
2L:23 -L:88

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Ser L:7 -Pro L:8

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IIF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IIF)

(-) Exons   (0, 0)

(no "Exon" information available for 1IIF)

(-) Sequences/Alignments

Theoretical Model
   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 H from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.eee.......eeeee..........eeeeee......eeeeee............................eee....hhhhh.eeeee.........eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1iif H   1 QDQLQQSGAELVRPGASVKLSCKALGYIFTDYEIHWVKQTPVHGLEWIGGIHPGSSGTAYNQKFKGKATLTADKSSTTAFMELSSLTSEDSAVYYCTRKDYWGQGTTVTVSS 112
                                    10        20        30        40        50        60        70        80        90       100       110  


Chain L from PDB  Type:PROTEIN  Length:107
 aligned with KV5A5_MOUSE | P01637 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:107
                                    30        40        50        60        70        80        90       100       110       120       
          KV5A5_MOUSE    21 DIKMTQSPSSMYASLGERVTISCKASQDINSYLTWFQQKPGKSPKTLLYRANRLVDGVPSRFSGSGSGQDFSLTISSLEYEDMGIYYCLQYDEFPLTFGAGTKLELK 127
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee........eeee.......eeeeee.........ee...ee.......ee..ee..ee..ee........eeeeeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1iif L   1 DIKMTQSPSSMYTSLGERVTITCKASQDINSFLTWFLQKPGKSPKTLIYRANRLMIGVPSRFSGSGSGQTYSLTISSLEYEDMGIYYCLQYDDFPLTFGAGTKLDLK 107
                                    10        20        30        40        50        60        70        80        90       100       


Chain P from PDB  Type:PROTEIN  Length:11
 aligned with GAG_HV1Z2 | P12495 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:11
                                   188 
            GAG_HV1Z2   179 GATPQDLNTML 189
               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
                 1iif P   1 GATPQDLNTML  11
                                    10
   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 1IIF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1IIF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IIF)

(-) Gene Ontology  (21, 21)

Theoretical Model(hide GO term definitions)
Chain L   (KV5A5_MOUSE | P01637)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

Chain P   (GAG_HV1Z2 | P12495)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0046755    viral budding    A viral process by which enveloped viruses acquire a host-derived membrane enriched in viral proteins to form their external envelope. The process starts when nucleocapsids, assembled or in the process of being built, induce formation of a membrane curvature in the host plasma or organelle membrane and wrap up in the forming bud. The process ends when the bud is eventually pinched off by membrane scission to release the enveloped particle into the lumenal or extracellular space.
    GO:0039702    viral budding via host ESCRT complex    Viral budding which uses a host ESCRT protein complex, or complexes, to mediate the budding process.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0072494    host multivesicular body    A late endosome in which regions of the limiting host cell endosomal membrane invaginate to form internal vesicles; host membrane proteins that enter the internal vesicles are sequestered from the host cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019013    viral nucleocapsid    The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

 Visualization

(-) Interactive Views

Theoretical Model
  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
(no "Ligands, Modified Residues, Ions" information available for 1iif)
 
  Sites
(no "Sites" information available for 1iif)
 
  Cis Peptide Bonds
    Ser L:7 - Pro L:8   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Theoretical Model 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
  1iif
    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
  GAG_HV1Z2 | P12495
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  KV5A5_MOUSE | P01637
    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
  GAG_HV1Z2 | P12495
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  KV5A5_MOUSE | P01637
    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
        GAG_HV1Z2 | P12495: 1sje 1sjh 3d3t

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1IIF)