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(-) Description

Title :  IGG1 FAB FRAGMENT (58.2) COMPLEX WITH 24-RESIDUE PEPTIDE (RESIDUES 308-333 OF HIV-1 GP120 (MN ISOLATE) WITH ALA TO AIB SUBSTITUTION AT POSITION 323
 
Authors :  R. L. Stanfield, E. Cabezas, A. C. Satterthwait, E. A. Stura, A. T. Profy, I. A. Wilson
Date :  21 Oct 98  (Deposition) - 02 Feb 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Immunoglobulin, Fab, Hiv-1, Gp120, V3, Viral Protein/Immune System Complex (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 (IGG1 ANTIBODY 58.2 (LIGHT CHAIN))
    ChainsL
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    StrainBALB-C
    SynonymFAB 58.2
 
Molecule 2 - PROTEIN (IGG1 ANTIBODY 58.2 (HEAVY CHAIN))
    ChainsH
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    StrainBALB-C
    SynonymFAB 58.2
 
Molecule 3 - PROTEIN (EXTERIOR MEMBRANE GLYCOPROTEIN(GP120))
    ChainsP
    EngineeredYES
    FragmentRESIDUES 308-332 FROM HIV-1 GP120
    MutationYES
    Other DetailsTHE MOLECULE WAS CHEMICALLY SYNTHESIZED
    SynonymV3 LOOP
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit HLP

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1AIB1Mod. Amino AcidALPHA-AMINOISOBUTYRIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 1F58)

(-) 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 1F58)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F58)

(-) Exons   (0, 0)

(no "Exon" information available for 1F58)

(-) 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 Q99LC4_MOUSE | Q99LC4 from UniProtKB/TrEMBL  Length:463

    Alignment length:229
                                                          50                                                                                                                                                                                                     
                                                        49 |                                                                           128    129                                                                                                                
                                    29        39        49 |      58        68        78        88        98       108       118       128      |132       142       152       162       172       182       192       202       212       222       232         
        Q99LC4_MOUSE     20 QVQLQQSGAELARPGASVRLSCKASGYTFT-GYGVSWVKQRTGQGLEWVGEIYPGSGNTYYSEKFKGKATLTTDKSSSTAYMHLSSLTSEDSAVYFCARSSYYSYDLFAY------WGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC  241
               SCOP domains d1f58h1 H:1-113 Immunoglobulin heavy chain variable domai n, VH                                                                d1f58h2 H:114-230 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 1f58H01 H:1-113 Immunoglobulins                                                                                                1f58H02 H:114-227 Immunoglobulins                                                                  --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........eeeeeeee........eeeeeee.....eeeeeeee....-eee....hhheeeeee....eeeeee....hhh.eeeeeeeeeeeee...eeeeeeeee...eee..........eeeee..........eeeeeeeeeee.....eeeehhh.....eee...eee..eeeeeeeeeee........eeeeeeehhh.eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1f58 H    1 DVQLQQSGPDLVKPSQSLSLTCTVTGYSITSGYSWHWIRQFPGNKLEWMGYIHYSAG-TNYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCAREEAMPYGNQAYYYAMDCWGQGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC  230
                                    10        20        30     |  39        49      | 58        68        78    ||| 85        95     |100E||||   106       116       126   ||  138       148     ||163     ||174     ||186       196| ||   209       219   ||    
                                                             35A                   56 |                       82A||               100A||||||||                           130|                  154|||    169|      180|          196| || 206|            223|    
                                                                                     57                        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:216
 aligned with KV3AE_MOUSE | P01666 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:216
                                                                                                                                        111                                                                                                         
                                    10        20        30        40        50        60        70        80        90       100       110|        -         -         -         -         -         -         -         -         -         -      
         KV3AE_MOUSE      1 DIVLTQSPASLAVSLGQRATISCKASQSVDYDGDSYMNWYQQKPGQPPKLLIYAASNLESGIPARFSGSGSGTDFTLNIHPVEEEDAATYYCQQSNEDPLTFGAGTKLELK---------------------------------------------------------------------------------------------------------    -
               SCOP domains d1f58l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                     d1f58l2 L:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1f58L01 L:1-108 Immunoglobulins                                                                                 1f58L02 L:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee...........eeeeee......eeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeee.......eeeee...hhhhhh.eeeeeeeee......eeeeeee..eee...eeeee...........eeeeeeeehhhhhh..eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1f58 L    1 DIVLTQSPASLAVSLGQRATISCKASQGVDFDGASFMNWYQQKPGQPPKLLIFAASTLESGIPARFSGRGSGTDFTLNIHPVEEEDAATYYCQQSHEDPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRA  212
                                    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
 aligned with ENV_HV1MN | P05877 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:11
                                   320 
           ENV_HV1MN    311 RIHIGPGRAFY  321
               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
                1f58 P  313 RIHIGPGRaFY  325
                               ||  324 
                             316|   |  
                              319   |  
                                  323-AIB

   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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F58)

(-) Gene Ontology  (44, 47)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (Q99LC4_MOUSE | Q99LC4)

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.

Chain P   (ENV_HV1MN | P05877)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
biological process
    GO:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    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:0019082    viral protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    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:0044175    host cell endosome membrane    The lipid bilayer surrounding a host cell endosome.
    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:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    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.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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  Cis Peptide Bonds
    Arg H:199 - Pro H:200   [ RasMol ]  
    Asp L:94 - Pro L:95   [ RasMol ]  
    Glu H:150 - Pro H:151   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1MN | P058771acy 1ai1 1ggi 1k5m 1nak 1niz 1nj0 1q1j 2b0s 2qsc 3e6h 3go1 3mlw 3mlx 3uji 4m1d 4xaw 4xbe 4xc1 4xc3 4xcf 4xmk
        IGH1M_MOUSE | P0186915c8 1a0q 1a3l 1acy 1ae6 1c12 1cic 1ck0 1cl7 1f11 1igy 1jhk 1jrh 1kc5 1kcr 1kcu 1ken 1l7t 1ors 1qfu 1ruq 1rur 1s5i 25c8 2ajs 2aju 2ajv 2ajx 2ajy 2ajz 2ak1
        KV3AE_MOUSE | P016662f58 3f58
        Q99LC4_MOUSE | Q99LC41afv 3hkf
UniProtKB/TrEMBL
        Q99LC4_MOUSE | Q99LC41ae6 1e6j 1gig 1jhk 1jnl 1jnn 2a1w 2ntf 2vir 2vis 2vit 4q0x

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1F58)