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(-) Description

Title :  HIV-1 IN CORE DOMAIN IN COMPLEX WITH 2,3-DIHYDRO-1,4-BENZODIOXIN-5-YLMETHANOL
 
Authors :  J. Wielens, D. K. Chalmers, M. W. Parker, M. J. Scanlon
Date :  29 Mar 12  (Deposition) - 30 Jan 13  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rnaseh, Dna Binding, Dna Cleavage, Dna Integration, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Wielens, S. J. Headey, D. I. Rhodes, R. J. Mulder, O. Dolezal, J. J. Deadman, J. Newman, D. K. Chalmers, M. W. Parker, T. S. Peat, M. J. Scanlon
Parallel Screening Of Low Molecular Weight Fragment Libraries: Do Differences In Methodology Affect Hit Identification?
J Biomol Screen V. 18 147 2013
PubMed-ID: 23139382  |  Reference-DOI: 10.1177/1087057112465979

(-) Compounds

Molecule 1 - POL POLYPROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET23B+
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentINTEGRASE CORE DOMAIN, UNP RESIDUES 770-927
    GenePOL
    MutationYES
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid11676
    StrainNL43

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1CD4Ligand/IonCADMIUM ION
2CL1Ligand/IonCHLORIDE ION
3DBJ1Ligand/Ion2,3-DIHYDRO-1,4-BENZODIOXIN-5-YLMETHANOL
4SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:65 , HIS A:67 , GLU A:92 , CD A:302 , HOH A:410 , ASP B:131BINDING SITE FOR RESIDUE CD A 301
2AC2SOFTWARECYS A:65 , GLU A:92 , ASP A:116 , CD A:301 , CL A:303 , HOH A:402 , ASP B:131BINDING SITE FOR RESIDUE CD A 302
3AC3SOFTWAREASP A:64 , CYS A:65 , LEU A:74 , ASP A:116 , PHE A:121 , CD A:302 , HOH A:401BINDING SITE FOR RESIDUE CL A 303
4AC4SOFTWARETHR A:66 , HIS A:67BINDING SITE FOR RESIDUE SO4 A 304
5AC5SOFTWAREGLU A:69 , ARG A:166 , GLU A:170 , HIS A:171 , LEU A:172 , ARG A:187 , ILE A:191BINDING SITE FOR RESIDUE SO4 A 305
6AC6SOFTWARETRP A:108 , ASN A:184 , HIS A:185 , GLY A:197 , VAL A:201 , HOH A:415 , GLY B:106 , ARG B:107 , TRP B:108 , PRO B:109 , ILE B:204BINDING SITE FOR RESIDUE DBJ A 306
7AC7SOFTWARECYS B:65 , GLU B:92 , ASP B:116 , CD B:302 , HOH B:402 , HOH B:413 , HOH B:414BINDING SITE FOR RESIDUE CD B 301
8AC8SOFTWARECYS B:65 , HIS B:67 , GLU B:92 , CD B:301 , HOH B:406 , HOH B:411 , HOH B:413BINDING SITE FOR RESIDUE CD B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VQP)

(-) 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:141
 aligned with Q72498_9HIV1 | Q72498 from UniProtKB/TrEMBL  Length:1003

    Alignment length:152
                                   780       790       800       810       820       830       840       850       860       870       880       890       900       910       920  
         Q72498_9HIV1   771 CSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATD 922
               SCOP domains d3vqpa_ A: Retroviral integrase, catalytic domain                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee..eeeeeeee.....eeeeee...hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh.eeee...-----------.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhee.....eehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vqp A  56 SSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACDWAGIKQEDGIP-----------MNKELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGGIGGYSAGERIVDIIATD 207
                                    65        75        85        95       105       115       125       135      |  -       155       165       175       185       195       205  
                                                                                                                142         154                                                     

Chain B from PDB  Type:PROTEIN  Length:140
 aligned with Q72498_9HIV1 | Q72498 from UniProtKB/TrEMBL  Length:1003

    Alignment length:152
                                   781       791       801       811       821       831       841       851       861       871       881       891       901       911       921  
         Q72498_9HIV1   772 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDI 923
               SCOP domains d3vqpb_ B: Retroviral integrase, catalytic domain                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee..eeeeeeee.....eeeeee...hhhhhhhhhhhhhhhh...eee........hhhhhhhhhhhh.eee------------.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhee.....eehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vqp B  57 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACDWAGIKQE------------IESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGGIGGYSAGERIVDIIATDI 208
                                    66        76        86        96       106       116       126       136 |       -    |  156       166       176       186       196       206  
                                                                                                           138          151                                                         

   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q72498_9HIV1 | Q72498)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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: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: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: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: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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q72498_9HIV1 | Q724981k6y 3ao2
UniProtKB/TrEMBL
        Q72498_9HIV1 | Q724983ao1 3ao3 3ao4 3ao5 3l3u 3l3v 3ovn 3vq4 3vq5 3vq6 3vq7 3vq8 3vq9 3vqa 3vqb 3vqc 3vqd 3vqe 3vqq 5hot

(-) Related Entries Specified in the PDB File

3l3u 3l3v 3ovn 3vq4 3vq5 3vq6 3vq7 3vq8 3vq9 3vqa 3vqb 3vqc 3vqd 3vqe 3vqq