PDB entry 6erf

View 6erf on RCSB PDB site
Description: complex of aplf factor and ku heterodimer bound to dna
Deposited on 2017-10-18, released 2018-10-17
The last revision was dated 2021-06-23, with a file datestamp of 2021-06-18.
Experiment type: XRAY
Resolution: 3.01 Å
R-factor: N/A
AEROSPACI score: 0.2 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: X-ray repair cross-complementing protein 6
    Species: Homo sapiens [TaxId:9606]
    Gene: XRCC6, G22P1
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: X-ray repair cross-complementing protein 5
    Species: Homo sapiens [TaxId:9606]
    Gene: XRCC5, G22P2
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: X-ray repair cross-complementing protein 6
    Species: Homo sapiens [TaxId:9606]
    Gene: XRCC6, G22P1
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: X-ray repair cross-complementing protein 5
    Species: Homo sapiens [TaxId:9606]
    Gene: XRCC5, G22P2
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: X-ray repair cross-complementing protein 6
    Species: Homo sapiens [TaxId:9606]
    Gene: XRCC6, G22P1
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: X-ray repair cross-complementing protein 5
    Species: Homo sapiens [TaxId:9606]
    Gene: XRCC5, G22P2
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: X-ray repair cross-complementing protein 6
    Species: Homo sapiens [TaxId:9606]
    Gene: XRCC6, G22P1
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: X-ray repair cross-complementing protein 5
    Species: Homo sapiens [TaxId:9606]
    Gene: XRCC5, G22P2
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: DNA (5'-d(*gp*tp*tp*tp*tp*tp*ap*gp*tp*tp*tp*ap*tp*tp*gp*gp*gp*cp*gp*cp*g)-3')
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'J':
    Compound: DNA (34-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'K':
    Compound: DNA (5'-d(*gp*tp*tp*tp*tp*tp*ap*gp*tp*tp*tp*ap*tp*tp*gp*gp*gp*cp*gp*cp*g)-3')
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'L':
    Compound: DNA (34-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'M':
    Compound: DNA (5'-d(*gp*tp*tp*tp*tp*tp*ap*gp*tp*tp*tp*ap*tp*tp*gp*gp*gp*cp*gp*cp*g)-3')
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'N':
    Compound: DNA (34-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'O':
    Compound: DNA (5'-d(*gp*tp*tp*tp*tp*tp*ap*gp*tp*tp*tp*ap*tp*tp*gp*gp*gp*cp*gp*cp*g)-3')
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'P':
    Compound: DNA (34-mer)
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'Q':
    Compound: Aprataxin and PNK-like factor
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
  • Chain 'R':
    Compound: Aprataxin and PNK-like factor
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
  • Chain 'S':
    Compound: Aprataxin and PNK-like factor
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
  • Chain 'T':
    Compound: Aprataxin and PNK-like factor
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
  • Heterogens: 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:
    >6erfA (A:)
msgwesyyktegdeeaeeeqeenleasgdykysgrdsliflvdaskamfesqsedeltpf
dmsiqciqsvyiskiissdrdllavvfygtekdknsvnfkniyvlqeldnpgakrileld
qfkgqqgqkrfqdmmghgsdyslsevlwvcanlfsdvqfkmshkrimlftnednphgnds
akasrartkagdlrdtgifldlmhlkkpggfdislfyrdiisiaededlrvhfeesskle
dllrkvraketrkralsrlklklnkdivisvgiynlvqkalkpppiklyretnepvktkt
rtfntstgglllpsdtkrsqiygsrqiilekeeteelkrfddpglmlmgfkplvllkkhh
ylrpslfvypeeslvigsstlfsallikclekevaalcrytprrnippyfvalvpqeeel
ddqkiqvtppgfqlvflpfaddkrkmpftekimatpeqvgkmkaiveklrftyrsdsfen
pvlqqhfrnlealaldlmepeqavdltlpkveamnkrlgslvdefkelvyppdynpegkv
tkrk

    Sequence, based on observed residues (ATOM records):
    >6erfA (A:)
rdsliflvdaskamfesqsedeltpfdmsiqciqsvyiskiissdrdllavvfygtekdk
nsvnfkniyvlqeldnpgakrileldqfkgqqgqkrfqdmmghgsdyslsevlwvcanlf
sdshkrimlftnednphgndsakasrartkagdlrdtgifldlmhlkkpggfdislfyrd
iisiaededlrvhfeesskledllrkvraketrkralsrlklklnkdivisvgiynlvqk
alkpppiklyretnepvktktrtfntstglpsdtkrsqiygsrqiilekeeteelkrfdd
pglmlmgfkplvllkkhhylrpslfvypeeslvigsstlfsallikclekevaalcrytp
rrnippyfvalvpqeeelddqkiqvtppgfqlvflpfaddkrkmpftekimatpeqvgkm
kaiveklrftyrsdsfenpvlqqhfrnlealaldlmepeqavdltlpkveamnkrlgslv
defkelvyppdyn

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6erfB (B:)
mhhhhhhhhhhenlyfqgvrsgnkaavvlcmdvgftmsnsipgiespfeqakkvitmfvq
rqvfaenkdeialvlfgtdgtdnplsggdqyqnitvhrhlmlpdfdlledieskiqpgsq
qadfldalivsmdviqhetigkkfekrhieiftdlssrfsksqldiiihslkkcdislqf
flpfslgkedgsgdrgdgpfrlgghgpsfplkgiteqqkegleivkmvmislegedglde
iysfseslrklcvfkkierhsihwpcrltigsnlsiriaayksilqervkktwtvvdakt
lkkediqketvyclndddetevlkediiqgfrygsdivpfskvdeeqmkyksegkcfsvl
gfckssqvqrrffmgnqvlkvfaarddeaaavalsslihalddldmvaivryaydkranp
qvgvafphikhnyeclvyvqlpfmedlrqymfsslknskkyapteaqlnavdalidsmsl
akkdektdtledlfpttkipnprfqrlfqcllhralhpreplppiqqhiwnmlnppaevt
tksqiplskiktlfplieakkkdqvtaqeifq

    Sequence, based on observed residues (ATOM records):
    >6erfB (B:)
nkaavvlcmdvgftmsnsipgiespfeqakkvitmfvqrqvfaenkdeialvlfgtdgtd
nplsggdqyqnitvhrhlmlpdfdlledieskiqpgsqqadfldalivsmdviqhetigk
kfekrhieiftdlssrfsksqldiiihslkkcdislqfflpfsldgpfrlgghkgiteqq
kegleivkmvmislegedgldeiysfseslrklcvfkkierhsihwpcrltigsnlsiri
aayksilqervkktwtvvdaktlkkediqketvyclndddetevlkediiqgfrygsdiv
pfskvdeeqmkyksegkcfsvlgfckssqvqrrffmgnqvlkvfaarddeaaavalssli
halddldmvaivryaydkranpqvgvafphikhnyeclvyvqlpfmedlrqymfsslkns
kkyapteaqlnavdalidsmslakkdektdtledlfpttkipnprfqrlfqcllhralhp
replppiqqhiwnmlnppaevttksqiplskiktlfpliea

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6erfC (C:)
msgwesyyktegdeeaeeeqeenleasgdykysgrdsliflvdaskamfesqsedeltpf
dmsiqciqsvyiskiissdrdllavvfygtekdknsvnfkniyvlqeldnpgakrileld
qfkgqqgqkrfqdmmghgsdyslsevlwvcanlfsdvqfkmshkrimlftnednphgnds
akasrartkagdlrdtgifldlmhlkkpggfdislfyrdiisiaededlrvhfeesskle
dllrkvraketrkralsrlklklnkdivisvgiynlvqkalkpppiklyretnepvktkt
rtfntstgglllpsdtkrsqiygsrqiilekeeteelkrfddpglmlmgfkplvllkkhh
ylrpslfvypeeslvigsstlfsallikclekevaalcrytprrnippyfvalvpqeeel
ddqkiqvtppgfqlvflpfaddkrkmpftekimatpeqvgkmkaiveklrftyrsdsfen
pvlqqhfrnlealaldlmepeqavdltlpkveamnkrlgslvdefkelvyppdynpegkv
tkrk

    Sequence, based on observed residues (ATOM records):
    >6erfC (C:)
rdsliflvdaskamfesqsedeltpfdmsiqciqsvyiskiissdrdllavvfygtekdk
nsvnfkniyvlqeldnpgakrileldqfkgqqgqkrfqdmmghgsdyslsevlwvcanlf
sdvshkrimlftnednphgndsakasrartkagdlrdtgifldlmhlkkpggfdislfyr
diisiaededlrvhfeesskledllrkvraketrkralsrlklklnkdivisvgiynlvq
kalkpppiklyretnepvktktrtfntstgglllpsdtkrsqiygsrqiilekeeteelk
rfddpglmlmgfkplvllkkhhylrpslfvypeeslvigsstlfsallikclekevaalc
rytprrnippyfvalvpqeeelddqkiqvtppgfqlvflpfaddkrkmpftekimatpeq
vgkmkaiveklrftyrsdsfenpvlqqhfrnlealaldlmepeqavdltlpkveamnkrl
gslvdefkelvyppdynpeg

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6erfD (D:)
mhhhhhhhhhhenlyfqgvrsgnkaavvlcmdvgftmsnsipgiespfeqakkvitmfvq
rqvfaenkdeialvlfgtdgtdnplsggdqyqnitvhrhlmlpdfdlledieskiqpgsq
qadfldalivsmdviqhetigkkfekrhieiftdlssrfsksqldiiihslkkcdislqf
flpfslgkedgsgdrgdgpfrlgghgpsfplkgiteqqkegleivkmvmislegedglde
iysfseslrklcvfkkierhsihwpcrltigsnlsiriaayksilqervkktwtvvdakt
lkkediqketvyclndddetevlkediiqgfrygsdivpfskvdeeqmkyksegkcfsvl
gfckssqvqrrffmgnqvlkvfaarddeaaavalsslihalddldmvaivryaydkranp
qvgvafphikhnyeclvyvqlpfmedlrqymfsslknskkyapteaqlnavdalidsmsl
akkdektdtledlfpttkipnprfqrlfqcllhralhpreplppiqqhiwnmlnppaevt
tksqiplskiktlfplieakkkdqvtaqeifq

    Sequence, based on observed residues (ATOM records):
    >6erfD (D:)
nkaavvlcmdvgftmsnsipgiespfeqakkvitmfvqrqvfaenkdeialvlfgtdgtd
nplsggdqyqnitvhrhlmlpdfdlledieskiqpgsqqadfldalivsmdviqhetigk
kfekrhieiftdlssrfsksqldiiihslkkcdislqfflpfslpfrlgghgkgiteqqk
egleivkmvmislegedgldeiysfseslrklcvfkkierhsihwpcrltigsnlsiria
ayksilqervkktwtvvdaktlkkediqketvyclndddetevlkediiqgfrygsdivp
fskvdeeqmkyksegkcfsvlgfckssqvqrrffmgnqvlkvfaarddeaaavalsslih
alddldmvaivryaydkranpqvgvafphikhnyeclvyvqlpfmedlrqymfsslknsk
kyapteaqlnavdalidsmslakkdektdtledlfpttkipnprfqrlfqcllhralhpr
eplppiqqhiwnmlnppaevttksqiplskiktlfpliea

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6erfE (E:)
msgwesyyktegdeeaeeeqeenleasgdykysgrdsliflvdaskamfesqsedeltpf
dmsiqciqsvyiskiissdrdllavvfygtekdknsvnfkniyvlqeldnpgakrileld
qfkgqqgqkrfqdmmghgsdyslsevlwvcanlfsdvqfkmshkrimlftnednphgnds
akasrartkagdlrdtgifldlmhlkkpggfdislfyrdiisiaededlrvhfeesskle
dllrkvraketrkralsrlklklnkdivisvgiynlvqkalkpppiklyretnepvktkt
rtfntstgglllpsdtkrsqiygsrqiilekeeteelkrfddpglmlmgfkplvllkkhh
ylrpslfvypeeslvigsstlfsallikclekevaalcrytprrnippyfvalvpqeeel
ddqkiqvtppgfqlvflpfaddkrkmpftekimatpeqvgkmkaiveklrftyrsdsfen
pvlqqhfrnlealaldlmepeqavdltlpkveamnkrlgslvdefkelvyppdynpegkv
tkrk

    Sequence, based on observed residues (ATOM records):
    >6erfE (E:)
rdsliflvdaskamfesqsedeltpfdmsiqciqsvyiskiissdrdllavvfygtekdk
nsvnfkniyvlqeldnpgakrileldqfkgqqgqkrfqdmmghgsdyslsevlwvcanlf
sdvqshkrimlftnednphgndsakasrartkagdlrdtgifldlmhlkkpggfdislfy
rdiisiaededlrvhfeesskledllrkvraketrkralsrlklklnkdivisvgiynlv
qkalkpppiklyretnepvktktrtfntstggllpsdtkrsqiygsrqiilekeeteelk
rfddpglmlmgfkplvllkkhhylrpslfvypeeslvigsstlfsallikclekevaalc
rytprrnippyfvalvpqeeelddqkiqvtppgfqlvflpfaddkrkmpftekimatpeq
vgkmkaiveklrftyrsdsfenpvlqqhfrnlealaldlmepeqavdltlpkveamnkrl
gslvdefkelvyppdyn

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6erfF (F:)
mhhhhhhhhhhenlyfqgvrsgnkaavvlcmdvgftmsnsipgiespfeqakkvitmfvq
rqvfaenkdeialvlfgtdgtdnplsggdqyqnitvhrhlmlpdfdlledieskiqpgsq
qadfldalivsmdviqhetigkkfekrhieiftdlssrfsksqldiiihslkkcdislqf
flpfslgkedgsgdrgdgpfrlgghgpsfplkgiteqqkegleivkmvmislegedglde
iysfseslrklcvfkkierhsihwpcrltigsnlsiriaayksilqervkktwtvvdakt
lkkediqketvyclndddetevlkediiqgfrygsdivpfskvdeeqmkyksegkcfsvl
gfckssqvqrrffmgnqvlkvfaarddeaaavalsslihalddldmvaivryaydkranp
qvgvafphikhnyeclvyvqlpfmedlrqymfsslknskkyapteaqlnavdalidsmsl
akkdektdtledlfpttkipnprfqrlfqcllhralhpreplppiqqhiwnmlnppaevt
tksqiplskiktlfplieakkkdqvtaqeifq

    Sequence, based on observed residues (ATOM records):
    >6erfF (F:)
nkaavvlcmdvgftmsnsipgiespfeqakkvitmfvqrqvfaenkdeialvlfgtdgtd
nplsggdqyqnitvhrhlmlpdfdlledieskiqpgsqqadfldalivsmdviqhetigk
kfekrhieiftdlssrfsksqldiiihslkkcdislqfflpfslgpfrlgghgpsfplkg
iteqqkegleivkmvmislegedgldeiysfseslrklcvfkkierhsihwpcrltigsn
lsiriaayksilqervkktwtvvdaktlkkediqketvyclndddetevlkediiqgfry
gsdivpfskvdeeqmkyksegkcfsvlgfckssqvqrrffmgnqvlkvfaarddeaaava
lsslihalddldmvaivryaydkranpqvgvafphikhnyeclvyvqlpfmedlrqymfs
slknskkyapteaqlnavdalidsmslakkdektdtledlfpttkipnprfqrlfqcllh
ralhpreplppiqqhiwnmlnppaevttksqiplskiktlfpliea

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6erfG (G:)
msgwesyyktegdeeaeeeqeenleasgdykysgrdsliflvdaskamfesqsedeltpf
dmsiqciqsvyiskiissdrdllavvfygtekdknsvnfkniyvlqeldnpgakrileld
qfkgqqgqkrfqdmmghgsdyslsevlwvcanlfsdvqfkmshkrimlftnednphgnds
akasrartkagdlrdtgifldlmhlkkpggfdislfyrdiisiaededlrvhfeesskle
dllrkvraketrkralsrlklklnkdivisvgiynlvqkalkpppiklyretnepvktkt
rtfntstgglllpsdtkrsqiygsrqiilekeeteelkrfddpglmlmgfkplvllkkhh
ylrpslfvypeeslvigsstlfsallikclekevaalcrytprrnippyfvalvpqeeel
ddqkiqvtppgfqlvflpfaddkrkmpftekimatpeqvgkmkaiveklrftyrsdsfen
pvlqqhfrnlealaldlmepeqavdltlpkveamnkrlgslvdefkelvyppdynpegkv
tkrk

    Sequence, based on observed residues (ATOM records):
    >6erfG (G:)
rdsliflvdaskamfesqsedeltpfdmsiqciqsvyiskiissdrdllavvfygtekdk
nsvnfkniyvlqeldnpgakrileldqfkgqqgqkrfqdmmghgsdyslsevlwvcanlf
sdshkrimlftnednphgndsakasrartkagdlrdtgifldlmhlkkpggfdislfyrd
iisiaededlrvhfeesskledllrkvraketrkralsrlklklnkdivisvgiynlvqk
alkpppiklyretnepvktktrtfntstgglllpsdtkrsqiygsrqiilekeeteelkr
fddpglmlmgfkplvllkkhhylrpslfvypeeslvigsstlfsallikclekevaalcr
ytprrnippyfvalvpqeeelddqkiqvtppgfqlvflpfaddkrkmpftekimatpeqv
gkmkaiveklrftyrsdsfenpvlqqhfrnlealaldlmepeqavdltlpkveamnkrlg
slvdefkelvyppdy

  • Chain 'H':
    Sequence, based on SEQRES records:
    >6erfH (H:)
mhhhhhhhhhhenlyfqgvrsgnkaavvlcmdvgftmsnsipgiespfeqakkvitmfvq
rqvfaenkdeialvlfgtdgtdnplsggdqyqnitvhrhlmlpdfdlledieskiqpgsq
qadfldalivsmdviqhetigkkfekrhieiftdlssrfsksqldiiihslkkcdislqf
flpfslgkedgsgdrgdgpfrlgghgpsfplkgiteqqkegleivkmvmislegedglde
iysfseslrklcvfkkierhsihwpcrltigsnlsiriaayksilqervkktwtvvdakt
lkkediqketvyclndddetevlkediiqgfrygsdivpfskvdeeqmkyksegkcfsvl
gfckssqvqrrffmgnqvlkvfaarddeaaavalsslihalddldmvaivryaydkranp
qvgvafphikhnyeclvyvqlpfmedlrqymfsslknskkyapteaqlnavdalidsmsl
akkdektdtledlfpttkipnprfqrlfqcllhralhpreplppiqqhiwnmlnppaevt
tksqiplskiktlfplieakkkdqvtaqeifq

    Sequence, based on observed residues (ATOM records):
    >6erfH (H:)
nkaavvlcmdvgftmsnsipgiespfeqakkvitmfvqrqvfaenkdeialvlfgtdgtd
nplsggdqyqnitvhrhlmlpdfdlledieskiqpgsqqadfldalivsmdviqhetigk
kfekrhieiftdlssrfsksqldiiihslkkcdislqfflpfslgpfrlgghgpsfplkg
iteqqkegleivkmvmislegedgldeiysfseslrklcvfkkierhsihwpcrltigsn
lsiriaayksilqervkktwtvvdaktlkkediqketvyclndddetevlkediiqgfry
gsdivpfskvdeeqmkyksegkcfsvlgfckssqvqrrffmgnqvlkvfaarddeaaava
lsslihalddldmvaivryaydkranpqvgvafphikhnyeclvyvqlpfmedlrqymfs
slknskkyapteaqlnavdalidsmslakkdektdtledlfpttkipnprfqrlfqcllh
ralhpreplppiqqhiwnmlnppaevttksqiplskiktlfpliea

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    No sequence available.

  • Chain 'L':
    No sequence available.

  • Chain 'M':
    No sequence available.

  • Chain 'N':
    No sequence available.

  • Chain 'O':
    No sequence available.

  • Chain 'P':
    No sequence available.

  • Chain 'Q':
    Sequence, based on SEQRES records:
    >6erfQ (Q:)
kqqpilaerkrilptwml

    Sequence, based on observed residues (ATOM records):
    >6erfQ (Q:)
aerkrilptwml

  • Chain 'R':
    Sequence, based on SEQRES records:
    >6erfR (R:)
kqqpilaerkrilptwml

    Sequence, based on observed residues (ATOM records):
    >6erfR (R:)
laerkrilptwml

  • Chain 'S':
    Sequence, based on SEQRES records:
    >6erfS (S:)
kqqpilaerkrilptwml

    Sequence, based on observed residues (ATOM records):
    >6erfS (S:)
aerkrilptwml

  • Chain 'T':
    Sequence, based on SEQRES records:
    >6erfT (T:)
kqqpilaerkrilptwml

    Sequence, based on observed residues (ATOM records):
    >6erfT (T:)
aerkrilptwml