Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE WILD TYPE HIV-1 PROTEASE WITH THE INHIBITOR, AMPRENAVIR
 
Authors :  C. A. Schiffer, M. N. L. Nalam
Date :  19 Sep 08  (Deposition) - 01 Sep 09  (Release) - 17 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protease Inhibitor, Drug Resistance, Amprenavir, Hiv Protease, Aids, Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. M. King, M. Prabu-Jeyabalan, R. M. Bandaranayake, M. N. Nalam, E. A. Nalivaika, A. Ozen, N. K. Yilmaz, C. A. Schiffer
Extreme Entropy-Enthalpy Compensation In A Drug-Resistant Variant Of Hiv-1 Protease.
Acs Chem. Biol. V. 7 1536 2012
PubMed-ID: 22712830  |  Reference-DOI: 10.1021/CB300191K

(-) Compounds

Molecule 1 - PROTEASE
    ChainsA, B
    EC Number3.4.23.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPXC35
    Expression System StrainTAP106
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 491-589
    GeneGAG-POL
    MutationYES
    Organism CommonHIV-1
    Organism Taxid11685
    StrainHXB2
    SynonymRETROPEPSIN, PR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
14781Ligand/Ion{3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL-2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YLESTER
2ACT4Ligand/IonACETATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , GLY A:48 , GLY A:49 , ILE A:50 , HOH A:108 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:30 , VAL B:32 , GLY B:48 , GLY B:49 , ILE B:50 , PRO B:81 , VAL B:82 , ILE B:84BINDING SITE FOR RESIDUE 478 A 200
2AC2SOFTWARELYS A:7 , HOH A:107BINDING SITE FOR RESIDUE ACT A 501
3AC3SOFTWARELYS A:20 , GLU A:21 , ASN A:83 , HOH A:530BINDING SITE FOR RESIDUE ACT A 502
4AC4SOFTWAREARG A:14 , GLY A:17 , GLY B:16 , HOH B:544BINDING SITE FOR RESIDUE ACT A 503
5AC5SOFTWAREGLY A:68 , HIS A:69 , LYS A:70 , PRO B:1BINDING SITE FOR RESIDUE ACT A 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ASP_PROT_RETROVPS50175 Aspartyl protease, retroviral-type family profile.POL_HV1A2510-579
 
  2A:20-89
B:20-89
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.POL_HV1A2512-523
 
  2A:22-33
B:22-33

(-) Exons   (0, 0)

(no "Exon" information available for 3EKV)

(-) 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 A from PDB  Type:PROTEIN  Length:99
 aligned with POL_HV1A2 | P03369 from UniProtKB/Swiss-Prot  Length:1437

    Alignment length:99
                                   500       510       520       530       540       550       560       570       580         
            POL_HV1A2   491 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 589
               SCOP domains d3ekva_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 3ekvA00 A:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------ASP_PROT_RETROV  PDB: A:20-89 UniProt: 510-579                        ---------- PROSITE (1)
                PROSITE (2) ---------------------ASP_PROTEASE------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3ekv A   1 PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF  99
                                    10        20        30        40        50        60        70        80        90         

Chain B from PDB  Type:PROTEIN  Length:99
 aligned with POL_HV1A2 | P03369 from UniProtKB/Swiss-Prot  Length:1437

    Alignment length:99
                                   500       510       520       530       540       550       560       570       580         
            POL_HV1A2   491 PQITLWQRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 589
               SCOP domains d3ekvb_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains 3ekvB00 B:1-99 Acid Proteases                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------ASP_PROT_RETROV  PDB: B:20-89 UniProt: 510-579                        ---------- PROSITE (1)
                PROSITE (2) ---------------------ASP_PROTEASE------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3ekv B   1 PQITLWKRPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF  99
                                    10        20        30        40        50        60        70        80        90         

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (POL_HV1A2 | P03369)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004523    RNA-DNA hybrid ribonuclease activity    Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
    GO:0003964    RNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004533    exoribonuclease H activity    Catalysis of the exonucleolytic cleavage of RNA to 5'-phosphomonoester oligonucleotides in both 5' to 3' and 3' to 5' directions.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino 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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0015074    DNA integration    The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006278    RNA-dependent DNA biosynthetic process    A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
    GO:0075713    establishment of integrated proviral latency    A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0039526    modulation by virus of host apoptotic process    Any process in which a virus modulates the frequency, rate or extent of apoptosis of infected host cells.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0039657    suppression by virus of host gene expression    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
    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:0075732    viral penetration into host nucleus    The crossing by the virus of the host nuclear membrane, either as naked viral genome or for small viruses as an intact capsid.
    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

Asymmetric/Biological Unit
  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
    478  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ekv)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3ekv
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  POL_HV1A2 | P03369
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.23.16
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  POL_HV1A2 | P03369
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        POL_HV1A2 | P033691aid 1b6j 1b6k 1b6l 1b6m 1b6p 1cpi 1d4k 1d4l 1f7a 1kj4 1kj7 1kjf 1kjg 1kjh 1kzk 1mt7 1mt8 1mt9 1mtb 1mtr 1n49 1t3r 1tsq 1tsu 1ytg 1yth 1z1h 1z1r 2aid 2f3k 2fgu 2fgv 2fns 2fnt 2j9j 2j9k 2je4 2nxd 2nxl 2nxm 2q3k 2qhy 2qhz 2qi0 2qi1 2qi3 2qi4 2qi5 2qi6 2qi7 3aid 3bxr 3bxs 3ekp 3ekq 3ekt 3ekw 3ekx 3eky 3el0 3el1 3el4 3el5 3el9 3em3 3em4 3em6 3fsm 3gi0 3gi4 3gi5 3gi6 3hau 3haw 3hbo 3hdk 3hlo 3hvp 3hzc 3i2l 3i7e 3iaw 3ka2 3lzv 3mxd 3mxe 3nwq 3nwx 3nxn 3nyg 3o9f 3o9g 3o9h 3o9i 3oxv 3oxw 3oxx 3oy4 3r4b 4ep2 4ep3 4epj 4eq0 4eqj 4f73 4f74 4f75 4f76 4hvp 4obd 4obf 4obg 4obh 4obj 4obk 4qj2 4qj6 4qj7 4qj8 4qj9 4qja 7hvp 8hvp

(-) Related Entries Specified in the PDB File

3ekp 3ekq 3ekt 3ekw 3ekx 3eky 3el0 3el1 3el4 3el5