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(-) Description

Title :  COMPLEX OF A CHIMERIC ALPHA/BETA-PEPTIDE BASED ON THE GP41 CHR DOMAIN BOUND TO A GP41 NHR DOMAIN PEPTIDE
 
Authors :  W. S. Horne, L. M. Johnson, S. H. Gellman
Date :  26 Jul 10  (Deposition) - 27 Jul 11  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Hiv Fusion Inhibitor, Mixed Alpha-Peptide/Beta-Peptide Backbone, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Johnson, W. S. Horne, S. H. Gellman
Broad Distribution Of Energetically Important Contacts Across An Extended Protein Interface.
J. Am. Chem. Soc. V. 133 10038 2011
PubMed-ID: 21644542  |  Reference-DOI: 10.1021/JA203358T

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN GP160
    Chains: A
    Engineered: YES
    Fragment: UNP RESIDUES 554 TO 589
    Organism Taxid: 32630
    Other Details: SYNTHETIC PEPTIDE
    Synthetic: YES
 
Molecule 2 - CHIMERIC ALPHA/BETA PEPTIDE BASED ON GP41 CHR DOMAIN SEQUENCE
    Chains: B
    Engineered: YES
    Organism Taxid: 32630
    Other Details: SYNTHETIC PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2B3E1Mod. Amino Acid(3S)-3-AMINOHEXANEDIOIC ACID
3GOL2Ligand/IonGLYCEROL
4XCP3Mod. Amino Acid(1S,2S)-2-AMINOCYCLOPENTANECARBOXYLIC ACID
5XPC2Mod. Amino Acid(3S,4R)-4-AMINOPYRROLIDINE-3-CARBOXYLIC ACID
Biological Unit 1 (5, 27)
No.NameCountTypeFull Name
1ACE3Mod. Amino AcidACETYL GROUP
2B3E3Mod. Amino Acid(3S)-3-AMINOHEXANEDIOIC ACID
3GOL6Ligand/IonGLYCEROL
4XCP9Mod. Amino Acid(1S,2S)-2-AMINOCYCLOPENTANECARBOXYLIC ACID
5XPC6Mod. Amino Acid(3S,4R)-4-AMINOPYRROLIDINE-3-CARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:16BINDING SITE FOR RESIDUE GOL A 38
2AC2SOFTWARESER A:1 , GLN B:27 , ARG B:36 , GLU B:37 , LEU B:38BINDING SITE FOR RESIDUE GOL B 40

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O3Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O3Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O3Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O3Z)

(-) Exons   (0, 0)

(no "Exon" information available for 3O3Z)

(-) Sequences/Alignments

Asymmetric 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:33
 aligned with Q9YP39_9HIV1 | Q9YP39 from UniProtKB/TrEMBL  Length:864

    Alignment length:33
                                   562       572       582   
         Q9YP39_9HIV1   553 LSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQ 585
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                 3o3z A   0 xSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQ  32
                            |        9        19        29   
                            |                                
                            0-ACE                            


Chain B from PDB  Type:PROTEIN  Length:36
                                                                    
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                 3o3z B   3 WExWDxAIAeYAxRIExLIxAAQEQQEKNEAALREL  38
                              |  |  12  |   | 22        32      
                              5-XCP  |  |   |  |                
                                 8-XPC  |   |  |                
                                    12-B3E  |  |                
                                       15-XCP  |                
                                           19-XCP               
                                              22-XPC
   Legend:   → Mismatch (orange background)
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    → 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 3O3Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O3Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O3Z)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9YP39_9HIV1 | Q9YP39)
molecular function
    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: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: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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9YP39_9HIV1 | Q9YP39: 3vie
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(-) Related Entries Specified in the PDB File

3o3x 3o3y 3o40 3o42 3o43