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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PRINCIPAL NEUTRALIZING SITE OF HIV-1
 
Authors :  J. B. Ghiara, I. A. Wilson
Date :  10 Feb 94  (Deposition) - 31 Jul 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Complex(Antibody/Hiv-1 Fragment) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. B. Ghiara, E. A. Stura, R. L. Stanfield, A. T. Profy, I. A. Wilson
Crystal Structure Of The Principal Neutralization Site Of Hiv-1.
Science V. 264 82 1994
PubMed-ID: 7511253
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGG1-KAPPA 59.1 FAB (LIGHT CHAIN)
    ChainsL
    EngineeredYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - IGG1-KAPPA 59.1 FAB (HEAVY CHAIN)
    ChainsH
    EngineeredYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 3 - HIV-1 GP120 (MN ISOLATE)
    ChainsP
    EngineeredYES
    FragmentFRAGMENT (RESIDUES 308 - 332)
    Organism Taxid11696

 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 1ACY)

(-) Sites  (0, 0)

(no "Site" information available for 1ACY)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:35 -H:52
3H:142 -H:208
4L:23 -L:88
5L:134 -L:194

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Asp 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 1ACY)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ACY)

(-) 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:221
                                                                                                                                                                                                                                                              
               SCOP domains d1acyh1 H:1-112 Immunoglobulin heavy chain variable domain, VH                                                          d1acyh2 H:113-226 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1acyH01 H:1-113 Immunoglobulins                                                                                          1acyH02 H:114-225 Immunoglobulins                                                                  - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeeee.....eeeeeeee....eee...hhh.eeeee.....eeeeee...hhhhheeeeeeeee.............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh.....eeeeeee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1acy H    1 QVKLQESGPAVIKPSQSLSLTCIVSGFSITRTNYCWHWIRQAPGKGLEWMGRICYEGSIYYSPSIKSRSTISRDTSLNKFFIQLISVTNEDTAMYYCSRENHMYETYFDVWGQGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPR  226
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     ||102       112       122       134       144       154|||    169|      180|      192   || |204 ||    215       225 
                                                             35A|                                             82A||               100A||                           130|                  154|||    169|      180|          196| || 206|                  
                                                              35B                                              82B|                100B|                            133                   156||     171       183           198 ||  208                  
                                                                                                                82C                 100C                                                   157|                               200|                       
                                                                                                                                                                                            162                                202                       

Chain L from PDB  Type:PROTEIN  Length:215
 aligned with KV3AB_MOUSE | P01663 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:215
                                                                                                                                        111                                                                                                        
                                    10        20        30        40        50        60        70        80        90       100       110|        -         -         -         -         -         -         -         -         -         -     
         KV3AB_MOUSE      1 NIVLTQSPASLAVSLGQRATISCRASESVDSYGNSFMHWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNEDPLTFGAGTKLELK--------------------------------------------------------------------------------------------------------    -
               SCOP domains d1acyl1 L:1-108 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1acyl2 L:109-211 Immunoglobulin light chain kappa constant domain, CL-kappa                            SCOP domains
               CATH domains 1acyL01 L:1-108 Immunoglobulins                                                                                 1acyL02 L:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee........ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1acy L    1 DIVMTQSPASLVVSLGQRATISCRASESVDSYGKSFMHWYQQKPGQPPKVLIYIASNLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNEDPPTFGAGTKLEMRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR  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:10
 aligned with ENV_HV1MN | P05877 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:10
                                   322
           ENV_HV1MN    313 HIGPGRAFYT  322
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ....hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                1acy P  315 HIGPGRAFYT  326
                             ||    326
                             ||       
                           316|       
                            319       

   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 1ACY)

(-) Gene Ontology  (44, 47)

Asymmetric/Biological Unit(hide GO term definitions)
Chain L   (KV3AB_MOUSE | P01663)
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:76 - Pro L:77   [ RasMol ]  
    Asp L:94 - Pro L:95   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1MN | P058771ai1 1f58 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 1ae6 1c12 1cic 1ck0 1cl7 1f11 1f58 1igy 1jhk 1jrh 1kc5 1kcr 1kcu 1ken 1l7t 1ors 1qfu 1ruq 1rur 1s5i 25c8 2ajs 2aju 2ajv 2ajx 2ajy 2ajz 2ak1

(-) Related Entries Specified in the PDB File

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