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(-) Description

Title :  SOLUTION STRUCTURE OF H12C MUTANT OF THE N-TERMINAL ZN BINDING DOMAIN OF HIV-1 INTEGRASE COMPLEXED TO CADMIUM, NMR, 40 STRUCTURES
 
Authors :  M. Cai, A. M. Gronenborn, G. M. Clore
Date :  11 Jun 98  (Deposition) - 16 Dec 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (40x)
Keywords :  Zn-Binding Protein, Aids, Polyprotein, Hydrolase, Aspartyl Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Cai, Y. Huang, M. Caffrey, R. Zheng, R. Craigie, G. M. Clore, A. M. Gronenborn
Solution Structure Of The His12 --> Cys Mutant Of The N-Terminal Zinc Binding Domain Of Hiv-1 Integrase Complexed To Cadmium.
Protein Sci. V. 7 2669 1998
PubMed-ID: 9865962
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HIV-1 INTEGRASE
    Cell LineBL21
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System GeneT7
    Expression System PlasmidPET-15B
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System VectorT7 RNA POLYMERASE
    Expression System Vector TypeT7
    GenePOTENTIAL
    MutationYES
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid11676

 Structural Features

(-) Chains, Units

  
NMR Structure (40x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:12 , CYS A:40 , CYS A:43BINDING SITE FOR RESIDUE CD A 56
2AC2SOFTWARECYS B:12 , CYS B:40 , CYS B:43BINDING SITE FOR RESIDUE CD B 56

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WJF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WJF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WJF)

(-) PROSITE Motifs  (2, 4)

NMR Structure (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_INTEGRASEPS50876 Zinc finger integrase-type profile.POL_HV1B51162-1203
 
  2A:3-44
B:3-44
2INTEGRASEPS50994 Integrase catalytic domain profile.POL_HV1B51213-1363
 
  2A:54-55
B:54-55

(-) Exons   (0, 0)

(no "Exon" information available for 1WJF)

(-) Sequences/Alignments

NMR Structure
   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:55
 aligned with POL_HV1B5 | P04587 from UniProtKB/Swiss-Prot  Length:1447

    Alignment length:55
                                  1169      1179      1189      1199      1209     
           POL_HV1B5   1160 FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVD 1214
               SCOP domains d1wjfa_ A:                                              SCOP domains
               CATH domains 1wjfA00 A:1-55  [code=1.10.10.200, no name defined]     CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE --ZF_INTEGRASE  PDB: A:3-44                 ---------IN PROSITE
                 Transcript ------------------------------------------------------- Transcript
                1wjf A    1 FLDGIDKAQEECEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVD   55
                                    10        20        30        40        50     

Chain B from PDB  Type:PROTEIN  Length:55
 aligned with POL_HV1B5 | P04587 from UniProtKB/Swiss-Prot  Length:1447

    Alignment length:55
                                  1169      1179      1189      1199      1209     
           POL_HV1B5   1160 FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVD 1214
               SCOP domains d1wjfb_ B:                                              SCOP domains
               CATH domains 1wjfB00 B:1-55  [code=1.10.10.200, no name defined]     CATH domains
           Pfam domains (1) -------Integrase_Zn-1wjfB01 B:8-47             -------- Pfam domains (1)
           Pfam domains (2) -------Integrase_Zn-1wjfB02 B:8-47             -------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE --ZF_INTEGRASE  PDB: B:3-44                 ---------IN PROSITE
                 Transcript ------------------------------------------------------- Transcript
                1wjf B    1 FLDGIDKAQEECEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVD   55
                                    10        20        30        40        50     

   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)

NMR Structure

(-) CATH Domains  (1, 2)

NMR Structure

(-) Pfam Domains  (1, 2)

NMR Structure

(-) Gene Ontology  (45, 45)

NMR Structure(hide GO term definitions)
Chain A,B   (POL_HV1B5 | P04587)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        POL_HV1B5 | P045871bdl 1bdq 1bdr 1fej 1ff0 1fff 1ffi 1fg6 1fg8 1fgc 1g2k 1hpv 1hvj 1hvs 1k1t 1k1u 1k2b 1k2c 1odx 1q9p 1tcx 1wje 2aoc 2aod 2aoe 2aof 2aog 2aoh 2aoi 2aoj 2avm 2avo 2avq 2avs 2avv 2bpv 2bpw 2bpx 2bpy 2bpz 2f80 2f81 2f8g 2g3l 2nmy 2nmz 2nnk 2nnp 2r38 2r3t 2r3w 2z54 3b7v 3b80 3bc4 3bgb 3bgc 3cyw 3cyx 3d1x 3d1y 3d1z 3d20 3oxc

(-) Related Entries Specified in the PDB File

1wje