PDB entry 5ld2

View 5ld2 on RCSB PDB site
Description: cryo-em structure of recbcd+dna complex revealing activated nuclease domain
Deposited on 2016-06-23, released 2016-10-05
The last revision was dated 2019-12-11, with a file datestamp of 2019-12-06.
Experiment type: EM
Resolution: 3.83 Å
R-factor: N/A
AEROSPACI score: 0.08 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'B':
    Compound: RecBCD enzyme subunit RecB,RecBCD enzyme subunit RecB,RecBCD enzyme subunit RecB
    Species: Escherichia coli (strain K12) [TaxId:83333]
    Gene: recB, ior, rorA, b2820, JW2788
    Database cross-references and differences (RAF-indexed):
    • Uniprot P08394 (Start-912)
    • PDB 5LD2 (913-End)
    • Uniprot P08394 (938-End)
      • engineered mutation (1080)
  • Chain 'C':
    Compound: RecBCD enzyme subunit RecC
    Species: Escherichia coli (strain K12) [TaxId:83333]
    Gene: recC, b2822, JW2790
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: RecBCD enzyme subunit RecD
    Species: Escherichia coli (strain K12) [TaxId:83333]
    Gene: recD, hopE, b2819, JW2787
    Database cross-references and differences (RAF-indexed):
  • Chain 'X':
    Compound: Fork-Hairpin DNA (70-MER)
    Species: Endothia gyrosa, synthetic [TaxId:40263]
  • Heterogens: ANP, MG

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.07, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'B':
    Sequence, based on SEQRES records:
    >5ld2B (B:)
    gmsdvaetldplrlplqgerlieasagtgktftiaalylrlllglggsaafprpltveel
    lvvtfteaataelrgrirsnihelriaclrettdnplyerlleeiddkaqaaqwlllaer
    qmdeaavftihgfcqrmlnlnafesgmlfeqqliedesllryqacadfwrrhcyplprei
    aqvvfetwkgpqallrdinrylqgeapvikapppddetlasrhaqivaridtvkqqwrda
    vgeldaliessgidrrkfnrsnqakwidkisawaeeetnsyqlpeslekfsqrfledrtk
    aggetprhplfeaidqllaeplsirdlvitralaeiretvarekrrrgelgfddmlsrld
    salrsesgevlaaairtrfpvamidefqdtdpqqyrifrriwhhqpetallligdpkqai
    yafrgadiftymkarsevhahytldtnwrsapgmvnsvnklfsqtddafmfreipfipvk
    sagknqalrfvfkgetqpamkmwlmegescgvgdyqstmaqvcaaqirdwlqagqrgeal
    lmngddarpvrasdisvlvrsrqeaaqvrdaltlleipsvylsnrdsvfetleaqemlwl
    lqavmtperentlrsalatsmmglnaldietlnndehawdvvveefdgyrqiwrkrgvmp
    mlralmsarniaenllataggerrltdilhisellqeagtqlesehalvrwlsqhilepd
    snassqqmrlesdkhlvqivtihkskgleyplvwlpfitnfrvqeqafyhdrhsfeavld
    lnaapesvdlaeaerlaedlrllyvaltrsvwhcslgvaplvrrrgdkkgdtdvhqsalg
    rllqkgepqdaaglrtciealcdddiawqtaqtgdnqpwqvndvstaelnaktlqrlpgd
    nwrvtsysglqqrxxxxxxxxxxxxxxxxxxxxxxxxxptltphqfprgaspgtflhslf
    edldftqpvdpnwvreklelggfesqwepvltewitavlqaplnetgvslsqlsarnkqv
    emefylpisepliasqldtlirqfdplsagcpplefmqvrgmlkgfidlvfrhegryyll
    ayksnwlgedssaytqqamaaamqahrydlqyqlytlalhrylrhriadydyehhfggvi
    ylflrgvdkehpqqgiyttrpnaglialmdemfagmtleea
    

    Sequence, based on observed residues (ATOM records):
    >5ld2B (B:)
    aetldplrlplqgerlieasagtgktftiaalylrlllglggsaafprpltveellvvtf
    teaataelrgrirsnihelriaclrettdnplyerlleeiddkaqaaqwlllaerqmdea
    avftihgfcqrmlnlnafesgmlfeqqliedesllryqacadfwrrhcyplpreiaqvvf
    etwkgpqallrdinrylqgeapvikapppddetlasrhaqivaridtvkqqwrdavgeld
    aliessgidrrkfnrsnqakwidkisawaeeetnsyqlpeslekftprhplfeaidqlla
    eplsirdlvitralaeiretvarekrrrgelgfddmlsrldsalrsesgevlaaairtrf
    pvamidefqdtdpqqyrifrriwhhqpetallligdpkqaiyafrgadiftymkarsevh
    ahytldtnwrsapgmvnsvnklfsqtddafmfreipfipvksagknqalrfvfkgetqpa
    mkmwlmegescgvgdyqstmaqvcaaqirdwlqagqrgeallmngddarpvrasdisvlv
    rsrqeaaqvrdaltlleipsvylsnrdsvfetleaqemlwllqavmtperentlrsalat
    smmglnaldietlnndehawdvvveefdgyrqiwrkrgvmpmlralmsarniaenllata
    ggerrltdilhisellqeagtqlesehalvrwlsqhilepdsnassqqmrlesdkhlvqi
    vtihkskgleyplvwlpfitnfrvqeqafyhdrhsfeavldlnaapesvdlaeaerlaed
    lrllyvaltrsvwhcslgvaplvrrrgdkkgdtdvhqsalgrllqkgepqdaaglrtcie
    alcdddiawqtaqtgdnqpwqvndvstaelnaktlqrlpgdnwrvtsysglqqrxxxxxx
    xxxxxxxxxxxxxxptltphqfprgaspgtflhslfedldftqpvdpnwvreklelggfe
    sqwepvltewitavlqaplnetgvslsqlsarnkqvemefylpisepliasqldtlirqf
    dplsagcpplefmqvrgmlkgfidlvfrhegryyllayksnwlgedssaytqqamaaamq
    ahrydlqyqlytlalhrylrhriadydyehhfggviylflrgvdkehpqqgiyttrpnag
    lialmdemfag
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >5ld2C (C:)
    mlrvyhsnrldvlealmefivererlddpfepemilvqstgmaqwlqmtlsqkfgiaani
    dfplpasfiwdmfvrvlpeipkesafnkqsmswklmtllpqlleredftllrhyltddsd
    krklfqlsskaadlfdqylvyrpdwlaqwetghlveglgeaqawqaplwkalveythqlg
    qprwhranlyqrfietlesattcppglpsrvficgisalppvylqalqalgkhieihllf
    tnpcryywgdikdpaylaklltrqrrhsfedrelplfrdsenagqlfnsdgeqdvgnpll
    aswgklgrdyiyllsdlessqeldafvdvtpdnllhniqsdilelenravagvnieefsr
    sdnkrpldpldssitfhvchspqrevevlhdrllamleedptltprdiivmvadidsysp
    fiqavfgsapadrylpyaisdrrarqshpvleafisllslpdsrfvsedvlalldvpvla
    arfditeeglrylrqwvnesgirwgidddnvrelelpatgqhtwrfgltrmllgyamesa
    qgewqsvlpydessgliaelvghlasllmqlniwrrglaqerpleewlpvcrdmlnaffl
    pdaeteaamtlieqqwqaiiaeglgaqygdavplsllrdelaqrldqerisqrflagpvn
    ictlmpmrsipfkvvcllgmndgvyprqlaplgfdlmsqkpkrgdrsrrdddrylfleal
    isaqqklyisyigrsiqdnserfpsvlvqelidyigqshylpgdealncdesearvkahl
    tclhtrmpfdpqnyqpgerqsyarewlpaasqagkahsefvqplpftlpetvpletlqrf
    wahpvraffqmrlqvnfrtedseipdtepfileglsryqinqqllnalveqddaerlfrr
    fraagdlpygafgeifwetqcqemqqladrviacrqpgqsmeidlacngvqitgwlpqvq
    pdgllrwrpsllsvaqgmqlwlehlvycasggngesrlflrkdgewrfpplaaeqalhyl
    sqliegyregmsapllvlpesggawlktcydaqndamldddstlqkartkflqayegnmm
    vrgegddiwyqrlwrqltpetmeaiveqsqrfllplfrfnqs
    

    Sequence, based on observed residues (ATOM records):
    >5ld2C (C:)
    mlrvyhsnrldvlealmefivererlddpfepemilvqstgmaqwlqmtlsqkfgiaani
    dfplpasfiwdmfvrvlpeipkesafnkqsmswklmtllpqlleredftllrhyltddsd
    krklfqlsskaadlfdqylvyrpdwlaqwetghlveglgeaqawqaplwkalveythqlg
    qprwhranlyqrfietlesattcppglpsrvficgisalppvylqalqalgkhieihllf
    tnpcryywgdikdpaylaklltrqrrhsfedrelplfrdsenagqlfnsdgeqdvgnpll
    aswgklgrdyiyllsdlessqeldafvdvtpdnllhniqsdilelenravagvnieefsr
    sdnkrpldpldssitfhvchspqrevevlhdrllamleedptltprdiivmvadidsysp
    fiqavfgsapadrylpyaisdrrarqshpvleafisllslpdsrfvsedvlalldvpvla
    arfditeeglrylrqwvnesgirwgidddnvrelelpatgqhtwrfgltrmllgyamesa
    qgewqsvlpydessgliaelvghlasllmqlniwrrglaqerpleewlpvcrdmlnaffl
    pdaeteaamtlieqqwqaiiaeglgaqygdavplsllrdelaqrldqerisqrflagpvn
    ictlmpmrsipfkvvcllgmndgvyprqlaplgfdlmsqkpkrgdrsrrdddrylfleal
    isaqqklyisyigrsiqdnserfpsvlvqelidyigqshylpgdealncdesearvkahl
    tclhtrmpfdpqnyqpgerqsyarewlpaasqagkahsefvqplpftlpetvpletlqrf
    wahpvraffqmrlqvnfrtedseipdtepfileglsryqinqqllnalveqddaerlfrr
    fraagdlpygafgeifwetqcqemqqladrviacrqpgqsmeidlacngvqitgwlpqvq
    pdgllrwrpsllsvaqgmqlwlehlvycasggngesrlflrkdgewrfpplaaeqalhyl
    sqliegyregmsapllvlpesggawlktcydaqndamldddstlqkartkflqayegnmm
    vrgegddiwyqrlwrqltpetmeaiveqsqrfllplfrfnq
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >5ld2D (D:)
    mgklqkqlleavehkqlrpldvqfaltvagdehpavtlaaallshdageghvclplsrle
    nneashpllatcvseigelqnweecllasqavsrgdeptpmilcgdrlylnrmwcnertv
    arffnevnhaievdeallaqtldklfpvsdeinwqkvaaavaltrrisvisggpgtgktt
    tvakllaaliqmadgercrirlaaptgkaaarlteslgkalrqlpltdeqkkripedast
    lhrllgaqpgsqrlrhhagnplhldvlvvdeasmidlpmmsrlidalpdharviflgdrd
    qlasveagavlgdicayanagftaerarqlsrltgthvpagtgteaaslrdslcllqksy
    rfgsdsgigqlaaainrgdktavktvfqqdftdiekrllqsgedyiamleealagygryl
    dllqaraepdliiqafneyqllcalregpfgvaglnerieqfmqqkrkihrhphsrwyeg
    rpvmiarndsalglfngdigialdrgqgtrvwfampdgniksvqpsrlpehettwamtvh
    ksqgsefdhaalilpsqrtpvvtrelvytavtrarrrlslyaderilsaaiatrterrsg
    laalfssre
    

    Sequence, based on observed residues (ATOM records):
    >5ld2D (D:)
    klqkqlleavehkqlrpldvqfaltvagdehpavtlaaallshdageghvclplsrlenn
    eashpllatcvseigelqnweecllasqavsrgdeptpmilcgdrlylnrmwcnertvar
    ffnevnhaievdeallaqtldklfpvsdeinwqkvaaavaltrrisvisggpgtgktttv
    akllaaliqmadgercrirlaaptgkaaarlteslgkalrqlpltdeqkkripedastlh
    rllgaqpgsqrlrhhagnplhldvlvvdeasmidlpmmsrlidalpdharviflgdrdql
    asveagavlgdicayanagftaerarqlsrltgthvpagtgteaaslrdslcllqksyrf
    gsdsgigqlaaainrgdktavktvfqqdftdiekrllqsgedyiamleealagygryldl
    lqaraepdliiqafneyqllcalregpfgvaglnerieqfmqqkrkihrhphsrwyegrp
    vmiarndsalglfngdigialdrgqgtrvwfampdgniksvqpsrlpehettwamtvhks
    qgsefdhaalilpsqrtpvvtrelvytavtrarrrlslyaderilsaaiatrterrsgla
    alfss
    

  • Chain 'X':
    No sequence available.