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(-) Description

Title :  IGG1 FAB FRAGMENT (58.2) COMPLEX WITH 12-RESIDUE CYCLIC PEPTIDE (INCLUDING RESIDUES 315-324 OF HIV-1 GP120 (MN ISOLATE); H315S MUTATION
 
Authors :  R. L. Stanfield, E. Cabezas, A. C. Satterthwait, E. A. Stura, A. T. Profy, I. A. Wilson
Date :  23 Oct 98  (Deposition) - 09 Feb 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Immunoglobulin, Fab, Hiv-1, Gp120, V3, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Stanfield, E. Cabezas, A. Satterthwait, E. Stura, A. Profy, I. Wilson
Dual Conformations For The Hiv-1 Gp120 V3 Loop In Complexes With Different Neutralizing Fabs.
Structure Fold. Des. V. 7 131 1999
PubMed-ID: 10368281  |  Reference-DOI: 10.1016/S0969-2126(99)80020-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (IMMUNOGLOBULIN GAMMA I (58.2))
    Chains: L
    Fragment: LIGHT CHAIN OF FAB
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
    Synonym: FAB 58.2
 
Molecule 2 - PROTEIN (IMMUNOGLOBULIN GAMMA I (58.2))
    Chains: H
    Fragment: HEAVY CHAIN OF FAB
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
    Synonym: FAB 58.2
 
Molecule 3 - PROTEIN (CYCLIC PEPTIDE (GP120))
    Chains: P
    Engineered: YES
    Fragment: RESIDUES 315-324 FROM HIV-1 GP120
    Mutation: YES
    Other Details: 12 RESIDUE HYDRAZONE-LINKED CYCLIC PEPTIDE WAS CHEMICALLY SYNTHESIZED FROM RESIDUES 316-324 OF HIV-1 GP120 STRAIN MN.
    Synonym: V3 LOOP
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3F58)

(-) Sites  (0, 0)

(no "Site" information available for 3F58)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2His L:76 -Pro L:77
3Asp L:94 -Pro L:95
4Tyr L:140 -Pro L:141
5Phe H:148 -Pro H:149
6Glu H:150 -Pro H:151
7Arg H:199 -Pro H:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F58)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F58)

(-) Exons   (0, 0)

(no "Exon" information available for 3F58)

(-) 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 H from PDB  Type:PROTEIN  Length:228
 aligned with HVM61_MOUSE | P18532 from UniProtKB/Swiss-Prot  Length:116

    Alignment length:228
                                                                                                                           116                                                                                                                                  
                                    28        38        48        58        68        78        88        98       108       | -         -         -         -         -         -         -         -         -         -         -         -         -        
         HVM61_MOUSE     19 DVQLQESGPDLVKPSQSLSLTCTVTGYSITSGYSWHWIRQFPGNKLEWMGYIHYSGNTSYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCAR----------------------------------------------------------------------------------------------------------------------------------    -
               SCOP domains d3f58h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                                d3f58h2 H:114-230 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 3f58H01 H:1-113 Immunoglobulins                                                                                               3f58H02 H:114-227 Immunoglobulins                                                                  --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.........eeeeeeee........eeeeeeee...eeeeeeeee....eee.......eeeeee....eeeeee....hhh.eeeeeeeeeeeee...eeeeeeeee...eee..........eeeee..........eeeeeeeeeee.....eeeehhh.....eeee........eeeeeeeeee..hhhh..eeeeeee....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3f58 H    1 DVQLQQSGPDLVKPSQSLSLTCTVTGYSITSGYSWHWIRQFPGNKLEWMGYIHYSAGTNYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCAREEAMPYGNQAYYYAMDCWGQGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC  230
                                    10        20        30     |  39        49        59        69        79   |||  86        96    ||100F|||    107       117       127  ||   139       149    |||164    || 175    || 187       198 ||   |210       220  ||    
                                                             35A                                             82A||               100A||||||||                           130|                  154|||    169|      180|          196| || 206|            223|    
                                                                                                              82B|                100B|||||||                            133                   156||     171       183           198 ||  208             226    
                                                                                                               82C                 100C||||||                                                   157|                               200|                         
                                                                                                                                    100D|||||                                                    162                                202                         
                                                                                                                                     100E||||                                                                                                                   
                                                                                                                                      100F|||                                                                                                                   
                                                                                                                                       100G||                                                                                                                   
                                                                                                                                        100H|                                                                                                                   
                                                                                                                                         100I                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:215
 aligned with KV3AE_MOUSE | P01666 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:215
                                                                                                                                        111                                                                                                        
                                    10        20        30        40        50        60        70        80        90       100       110|        -         -         -         -         -         -         -         -         -         -     
         KV3AE_MOUSE      1 DIVLTQSPASLAVSLGQRATISCKASQSVDYDGDSYMNWYQQKPGQPPKLLIYAASNLESGIPARFSGSGSGTDFTLNIHPVEEEDAATYYCQQSNEDPLTFGAGTKLELK--------------------------------------------------------------------------------------------------------    -
               SCOP domains d3f58l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                     d3f58l2 L:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 3f58L01 L:1-108 Immunoglobulins                                                                                 3f58L02 L:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee...........eeeeee......eeee.............eeeeee..eeeeee....hhh..eeeeee............eeeee......eeeee...hhhhh..eeeeeeeee......eeeeeee........eeeee...........eeeeeeeehhhhhh..eeeeeeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3f58 L    1 DIVLTQSPASLAVSLGQRATISCKASQGVDFDGASFMNWYQQKPGQPPKLLIFAASTLESGIPARFSGRGSGTDFTLNIHPVEEEDAATYYCQQSHEDPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  211
                                    10        20       27C|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206     
                                                     27A|||                                                                                                                                                                                        
                                                      27B||                                                                                                                                                                                        
                                                       27C|                                                                                                                                                                                        
                                                        27D                                                                                                                                                                                        


Chain P 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
                3f58 P  315 SIGPGRAFGGG   12
                             ||    |11 
                           316|  324|  
                            319    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  (4, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F58)

(-) Gene Ontology  (1, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (HVM61_MOUSE | P18532)
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 L   (KV3AE_MOUSE | P01666)
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.

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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 3f58)
 
  Cis Peptide Bonds
    Arg H:199 - Pro H:200   [ RasMol ]  
    Asp L:94 - Pro L:95   [ RasMol ]  
    Glu H:150 - Pro H:151   [ RasMol ]  
    His L:76 - Pro L:77   [ RasMol ]  
    Phe H:148 - Pro H:149   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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  3f58
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  KV3AE_MOUSE | P01666
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 Related Entries

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

UniProtKB/Swiss-Prot
        HVM61_MOUSE | P18532: 1kcs 1kcv 2exp 2exq 2f58
        KV3AE_MOUSE | P01666: 1f58 2f58

(-) Related Entries Specified in the PDB File

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