PDB entry 6ikg

View 6ikg on RCSB PDB site
Description: crystal structure of substrate-bound s9 peptidase (s514a mutant) from deinococcus radiodurans
Deposited on 2018-10-16, released 2018-11-14
The last revision was dated 2019-11-20, with a file datestamp of 2019-11-15.
Experiment type: XRAY
Resolution: 2.3 Å
R-factor: N/A
AEROSPACI score: 0.24 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Acyl-peptide hydrolase, putative
    Species: Deinococcus radiodurans R1 [TaxId:243230]
    Gene: DR_0165
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9RXY9 (Start-655)
      • engineered mutation (514)
  • Chain 'B':
    Compound: Acyl-peptide hydrolase, putative
    Species: Deinococcus radiodurans R1 [TaxId:243230]
    Gene: DR_0165
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9RXY9 (Start-655)
      • engineered mutation (514)
  • Chain 'C':
    Compound: Acyl-peptide hydrolase, putative
    Species: Deinococcus radiodurans R1 [TaxId:243230]
    Gene: DR_0165
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9RXY9 (Start-655)
      • engineered mutation (514)
  • Chain 'D':
    Compound: Acyl-peptide hydrolase, putative
    Species: Deinococcus radiodurans R1 [TaxId:243230]
    Gene: DR_0165
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9RXY9 (Start-655)
      • engineered mutation (514)
  • Chain 'E':
    Compound: met-ala-ala
    Species: DEINOCOCCUS RADIODURANS, synthetic [TaxId:1299]
    Database cross-references and differences (RAF-indexed):
    • PDB 6IKG (0-2)
  • Chain 'F':
    Compound: met-ala-ala
    Species: DEINOCOCCUS RADIODURANS, synthetic [TaxId:1299]
    Database cross-references and differences (RAF-indexed):
    • PDB 6IKG (0-2)
  • Heterogens: GOL, HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6ikgA (A:)
    gsnnsetpapgpdsllalafpsdpqvspdgkqvafvlaqiseedpakpdkdfarpryrsg
    lwlseggaarplthaetgrgdsaprwspdgqnlafvrsagevkaalmllplkggearrvt
    hfkngvsgpqwspdgrfiaftttadtedkrdergearvltrpvyrangadwlperpaalw
    lydveadklrewyapeigigalswwpdsrgvlivqsedewqasqwrqdvydlplptadap
    aapqklldwnsaahglaphpdgqrfaligrpagkgntehahlyliengqhrrldtghdhp
    vgdavggdchvgafpegprwldgdtllfsstvrgsvglftahigggvkaydhdpqgvisa
    ftanehgvaliresatrfpevelngqrvtdlharfpfpvrepqrvtfetelgegegwvll
    pegeqkvpallnihggphtdyghgfthefqlmaargygvcysnprgsvgygqawvdaiyg
    rwgtvdaddllnffdrcleavprldaaktavmggayggfmtnwitghttrfqaaitdrci
    snlisfggtsdiglrfwddelgldfsrradalklwdlsplqyvenvktptlivhsvldhr
    cpveqaeqwyaalhkhqvpvrfvrfpeenhelsrsgrpdrrltrlneyfawlerwl
    

    Sequence, based on observed residues (ATOM records):
    >6ikgA (A:)
    papgpdsllalafpsdpqvspdgkqvafvlaqiseedpakpdkdfarpryrsglwlsegg
    aarplthaetgrgdsaprwspdgqnlafvrsaalmllplkggearrvthfkngvsgpqws
    pdgrfiaftttadtedkrdergearvltrpvyrangadwlperpaalwlydveadklrew
    yapeigigalswwpdsrgvlivqsedewqasqwrqdvydlplptadapaapqklldwnsa
    ahglaphpdgqrfaligrpagkgntehahlyliengqhrrldtghdhpvgdavggdchvg
    afpegprwldgdtllfsstvrgsvglftahigggvkaydhdpqgvisaftanehgvalir
    esatrfpevelngqrvtdlharfpfpvrepqrvtfetelgegegwvllpegeqkvpalln
    ihggphtdyghgfthefqlmaargygvcysnprgsvgygqawvdaiygrwgtvdaddlln
    ffdrcleavprldaaktavmggayggfmtnwitghttrfqaaitdrcisnlisfggtsdi
    glrfwddelgldfsrradalklwdlsplqyvenvktptlivhsvldhrcpveqaeqwyaa
    lhkhqvpvrfvrfpeenhelsrsgrpdrrltrlneyfawlerwl
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6ikgB (B:)
    gsnnsetpapgpdsllalafpsdpqvspdgkqvafvlaqiseedpakpdkdfarpryrsg
    lwlseggaarplthaetgrgdsaprwspdgqnlafvrsagevkaalmllplkggearrvt
    hfkngvsgpqwspdgrfiaftttadtedkrdergearvltrpvyrangadwlperpaalw
    lydveadklrewyapeigigalswwpdsrgvlivqsedewqasqwrqdvydlplptadap
    aapqklldwnsaahglaphpdgqrfaligrpagkgntehahlyliengqhrrldtghdhp
    vgdavggdchvgafpegprwldgdtllfsstvrgsvglftahigggvkaydhdpqgvisa
    ftanehgvaliresatrfpevelngqrvtdlharfpfpvrepqrvtfetelgegegwvll
    pegeqkvpallnihggphtdyghgfthefqlmaargygvcysnprgsvgygqawvdaiyg
    rwgtvdaddllnffdrcleavprldaaktavmggayggfmtnwitghttrfqaaitdrci
    snlisfggtsdiglrfwddelgldfsrradalklwdlsplqyvenvktptlivhsvldhr
    cpveqaeqwyaalhkhqvpvrfvrfpeenhelsrsgrpdrrltrlneyfawlerwl
    

    Sequence, based on observed residues (ATOM records):
    >6ikgB (B:)
    apgpdsllalafpsdpqvspdgkqvafvlaqiseedpakpdkdfarpryrsglwlsegga
    arplthaetgrgdsaprwspdgqnlafvrsavkaalmllplkggearrvthfkngvsgpq
    wspdgrfiaftttadtedkrdergearvltrpvyrangadwlperpaalwlydveadklr
    ewyapeigigalswwpdsrgvlivqsedewqasqwrqdvydlplpapqklldwnsaahgl
    aphpdgqrfaligrpagkgntehahlyliengqhrrldtghdhpvgdavggdchvgafpe
    gprwldgdtllfsstvrgsvglftahigggvkaydhdpqgvisaftanehgvaliresat
    rfpevelngqrvtdlharfpfpvrepqrvtfetelgegegwvllpegeqkvpallnihgg
    phtdyghgfthefqlmaargygvcysnprgsvgygqawvdaiygrwgtvdaddllnffdr
    cleavprldaaktavmggayggfmtnwitghttrfqaaitdrcisnlisfggtsdiglrf
    wddelgldfsrradalklwdlsplqyvenvktptlivhsvldhrcpveqaeqwyaalhkh
    qvpvrfvrfpeenhelsrsgrpdrrltrlneyfawlerwl
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6ikgC (C:)
    gsnnsetpapgpdsllalafpsdpqvspdgkqvafvlaqiseedpakpdkdfarpryrsg
    lwlseggaarplthaetgrgdsaprwspdgqnlafvrsagevkaalmllplkggearrvt
    hfkngvsgpqwspdgrfiaftttadtedkrdergearvltrpvyrangadwlperpaalw
    lydveadklrewyapeigigalswwpdsrgvlivqsedewqasqwrqdvydlplptadap
    aapqklldwnsaahglaphpdgqrfaligrpagkgntehahlyliengqhrrldtghdhp
    vgdavggdchvgafpegprwldgdtllfsstvrgsvglftahigggvkaydhdpqgvisa
    ftanehgvaliresatrfpevelngqrvtdlharfpfpvrepqrvtfetelgegegwvll
    pegeqkvpallnihggphtdyghgfthefqlmaargygvcysnprgsvgygqawvdaiyg
    rwgtvdaddllnffdrcleavprldaaktavmggayggfmtnwitghttrfqaaitdrci
    snlisfggtsdiglrfwddelgldfsrradalklwdlsplqyvenvktptlivhsvldhr
    cpveqaeqwyaalhkhqvpvrfvrfpeenhelsrsgrpdrrltrlneyfawlerwl
    

    Sequence, based on observed residues (ATOM records):
    >6ikgC (C:)
    papgpdsllalafpsdpqvspdgkqvafvlaqiseepdkdfarpryrsglwlseggaarp
    lthaetgrgdsaprwspdgqnlafvrsavkaalmllplkggearrvthfkngvsgpqwsp
    dgrfiaftttadtedkrdergearvltrpvyrangadwlperpaalwlydveadklrewy
    apeigigalswwpdsrgvlivqsedewqasqwrqdvydlplptapaapqklldwnsaahg
    laphpdgqrfaligrpagkgntehahlyliengqhrrldtghdhpvgdavggdchvgafp
    egprwldgdtllfsstvrgsvglftahigggvkaydhdpqgvisaftanehgvaliresa
    trfpevelngqrvtdlharfpfpvrepqrvtfetelgegegwvllpegeqkvpallnihg
    gphtdyghgfthefqlmaargygvcysnprgsvgygqawvdaiygrwgtvdaddllnffd
    rcleavprldaaktavmggayggfmtnwitghttrfqaaitdrcisnlisfggtsdiglr
    fwddelgldfsrradalklwdlsplqyvenvktptlivhsvldhrcpveqaeqwyaalhk
    hqvpvrfvrfpeenhelsrsgrpdrrltrlneyfawlerwl
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6ikgD (D:)
    gsnnsetpapgpdsllalafpsdpqvspdgkqvafvlaqiseedpakpdkdfarpryrsg
    lwlseggaarplthaetgrgdsaprwspdgqnlafvrsagevkaalmllplkggearrvt
    hfkngvsgpqwspdgrfiaftttadtedkrdergearvltrpvyrangadwlperpaalw
    lydveadklrewyapeigigalswwpdsrgvlivqsedewqasqwrqdvydlplptadap
    aapqklldwnsaahglaphpdgqrfaligrpagkgntehahlyliengqhrrldtghdhp
    vgdavggdchvgafpegprwldgdtllfsstvrgsvglftahigggvkaydhdpqgvisa
    ftanehgvaliresatrfpevelngqrvtdlharfpfpvrepqrvtfetelgegegwvll
    pegeqkvpallnihggphtdyghgfthefqlmaargygvcysnprgsvgygqawvdaiyg
    rwgtvdaddllnffdrcleavprldaaktavmggayggfmtnwitghttrfqaaitdrci
    snlisfggtsdiglrfwddelgldfsrradalklwdlsplqyvenvktptlivhsvldhr
    cpveqaeqwyaalhkhqvpvrfvrfpeenhelsrsgrpdrrltrlneyfawlerwl
    

    Sequence, based on observed residues (ATOM records):
    >6ikgD (D:)
    apgpdsllalafpsdpqvspdgkqvafvlaqiseedpakpdkdfarpryrsglwlsegga
    arplthaetgrgdsaprwspdgqnlafvrsavkaalmllplkggearrvthfkngvsgpq
    wspdgrfiaftttadtedkrdergearvltrpvyrangadwlperpaalwlydveadklr
    ewyapeigigalswwpdsrgvlivqsedewqasqwrqdvydlplpapaapqklldwnsaa
    hglaphpdgqrfaligrpagkgntehahlyliengqhrrldtghdhpvgdavggdchvga
    fpegprwldgdtllfsstvrgsvglftahivkaydhdpqgvisaftanehgvaliresat
    rfpevelngqrvtdlharfpfpvrepqrvtfetelgegegwvllpegeqkvpallnihgg
    phtdyghgfthefqlmaargygvcysnprgsvgygqawvdaiygrwgtvdaddllnffdr
    cleavprldaaktavmggayggfmtnwitghttrfqaaitdrcisnlisfggtsdiglrf
    wddelgldfsrradalklwdlsplqyvenvktptlivhsvldhrcpveqaeqwyaalhkh
    qvpvrfvrfpeenhelsrsgrpdrrltrlneyfawlerwl
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records:
    >6ikgE (E:)
    maa
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records:
    >6ikgF (F:)
    maa