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(-) Description

Title :  INTERROGATING HIV INTEGRASE FOR COMPOUNDS THAT BIND- A SAMPL CHALLENGE
 
Authors :  T. S. Peat
Date :  11 Nov 13  (Deposition) - 20 Nov 13  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Structure Based Drug Design (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. S. Peat, O. Dolezal, J. Newman, D. Mobley, J. J. Deadman
Interrogating Hiv Integrase For Compounds That Bind- A Sampl Challenge.
J. Comput. Aided Mol. Des. V. 28 347 2014
PubMed-ID: 24532034  |  Reference-DOI: 10.1007/S10822-014-9721-7

(-) Compounds

Molecule 1 - INTEGRASE
    ChainsA, B
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorPET
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN, RESIDUES 50-212
    MutationYES
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid11676
    StrainTYPE1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
12SS2Ligand/Ion(2S)-6-[[[2-(CYCLOBUTYLMETHYLCARBAMOYL)PHENYL]METHYL-PROP-2-ENYL-AMINO]METHYL]-2-(3-HYDROXY-3-OXOPROPYL)-2,3-DIHYDRO-1,4-BENZODIOXINE-5-CARBOXYLIC ACID
2ACT2Ligand/IonACETATE ION
3CL2Ligand/IonCHLORIDE ION
4GOL2Ligand/IonGLYCEROL
5SO46Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR B:66 , HIS B:67 , LYS B:111 , LYS B:136 , LYS B:159BINDING SITE FOR RESIDUE SO4 B1210
02AC2SOFTWARETHR A:66 , HIS A:67 , LYS A:111 , LYS A:159 , HOH A:2008BINDING SITE FOR RESIDUE SO4 A1210
03AC3SOFTWARELYS B:71 , ARG B:166 , HIS B:171 , LEU B:172 , HOH B:2010 , HOH B:2064BINDING SITE FOR RESIDUE SO4 B1211
04AC4SOFTWARELYS A:71 , ARG A:166 , HIS A:171 , LEU A:172 , HOH A:2011 , HOH A:2081BINDING SITE FOR RESIDUE SO4 A1211
05AC5SOFTWAREGLU A:85 , ALA A:86 , PHE A:100 , LYS A:103 , HOH A:2021 , ARG B:107BINDING SITE FOR RESIDUE SO4 A1212
06AC6SOFTWAREARG A:107 , HOH A:2021 , GLU B:85 , ALA B:86 , PHE B:100 , LYS B:103BINDING SITE FOR RESIDUE SO4 B1212
07AC7SOFTWARETHR A:93 , GLY A:94 , GLN A:95 , THR A:125 , GOL A:1215 , HOH A:2033 , HOH A:2095BINDING SITE FOR RESIDUE ACT A1213
08AC8SOFTWARETHR B:93 , GLY B:94 , GLN B:95 , THR B:125 , GOL B:1215 , HOH B:2026 , HOH B:2027BINDING SITE FOR RESIDUE ACT B1213
09AC9SOFTWAREHIS B:185BINDING SITE FOR RESIDUE CL B1214
10BC1SOFTWAREHIS A:185BINDING SITE FOR RESIDUE CL A1214
11BC2SOFTWAREGLY A:94 , SER A:123 , THR A:124 , THR A:125 , ACT A:1213 , HOH A:2096 , GLN B:164BINDING SITE FOR RESIDUE GOL A1215
12BC3SOFTWAREGLN A:164 , HOH A:2075 , GLY B:94 , SER B:123 , THR B:124 , THR B:125 , ACT B:1213 , HOH B:2079BINDING SITE FOR RESIDUE GOL B1215
13BC4SOFTWAREGLN A:95 , GLU A:96 , TYR A:99 , ALA A:128 , HOH A:2032 , ASP B:167 , GLN B:168 , ALA B:169 , GLU B:170 , HIS B:171 , THR B:174 , MET B:178 , HOH B:2065 , HOH B:2081BINDING SITE FOR RESIDUE 2SS B1216
14BC5SOFTWAREASP A:167 , GLN A:168 , ALA A:169 , GLU A:170 , HIS A:171 , THR A:174 , MET A:178 , HOH A:2082 , HOH A:2097 , HOH A:2098 , GLN B:95 , GLU B:96 , TYR B:99 , ALA B:128BINDING SITE FOR RESIDUE 2SS A1216

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CEC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CEC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CEC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CEC)

(-) Exons   (0, 0)

(no "Exon" information available for 4CEC)

(-) 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:149
 aligned with Q76353_9HIV1 | Q76353 from UniProtKB/TrEMBL  Length:288

    Alignment length:153
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
         Q76353_9HIV1    57 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQ 209
               SCOP domains d4ceca_ A: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee..eeeeeeee.....eeeeee...hhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh.eee......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..----..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cec A  57 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRK----GYSAGERIVDIIATDIQ 209
                                    66        76        86        96       106       116       126       136       146       156       166       176       186 |    |196       206   
                                                                                                                                                             188  193                

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with Q76353_9HIV1 | Q76353 from UniProtKB/TrEMBL  Length:288

    Alignment length:153
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206   
         Q76353_9HIV1    57 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQ 209
               SCOP domains d4cecb_ B: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee..eeeeeeee.....eeeeee...hhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..----..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cec B  57 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRK----GYSAGERIVDIIATDIQ 209
                                    66        76        86        96       106       116       126       136       146       156       166       176       186 |    |196       206   
                                                                                                                                                             188  193                

   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 4CEC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CEC)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q76353_9HIV1 | Q76353)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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: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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q76353_9HIV1 | Q763531biz 1qs4 3nf6 3nf7 3nf8 3nf9 3nfa
UniProtKB/TrEMBL
        Q76353_9HIV1 | Q763531hyv 1hyz 3lpt 3lpu 3zcm 3zso 3zsq 3zsr 3zsv 3zsw 3zsx 3zsy 3zsz 3zt0 3zt1 3zt2 3zt3 3zt4 4ce9 4cea 4ceb 4ced 4cee 4cef 4ceo 4ceq 4cer 4ces 4cez 4cf0 4cf1 4cf2 4cf8 4cf9 4cfa 4cfb 4cfc 4cfd 4cgd 4cgf 4cgg 4cgh 4cgi 4cgj 4chn 4cho 4chp 4chq 4chy 4chz 4cie 4cif 4cig 4cj3 4cj4 4cj5 4cje 4cjf 4cjk 4cjl 4cjp 4cjq 4cjr 4cjs 4cjt 4cju 4cjv 4cjw 4ck1 4ck2 4ck3 4lh4 4lh5 4ovl 4y1c 4y1d 5kgw 5kgx 5krs 5krt 5u1c

(-) Related Entries Specified in the PDB File

4ce9 INTERROGATING HIV INTEGRASE FOR COMPOUNDS THAT BIND- A SAMPL CHALLENGE
4cea INTERROGATING HIV INTEGRASE FOR COMPOUNDS THAT BIND- A SAMPL CHALLENGE
4ceb INTERROGATING HIV INTEGRASE FOR COMPOUNDS THAT BIND- A SAMPL CHALLENGE
4ced INTERROGATING HIV INTEGRASE FOR COMPOUNDS THAT BIND- A SAMPL CHALLENGE
4cee INTERROGATING HIV INTEGRASE FOR COMPOUNDS THAT BIND- A SAMPL CHALLENGE
4cef INTERROGATING HIV INTEGRASE FOR COMPOUNDS THAT BIND- A SAMPL CHALLENGE