PDB entry 6l9z

View 6l9z on RCSB PDB site
Description: 338 bp di-nucleosome assembled with linker histone H1.X
Class: DNA binding protein
Keywords: Nucleosome, DNA-protein complex, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex, Linker Histone, H1.X
Deposited on 2019-11-11, released 2021-02-17
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-02-17, with a file datestamp of 2021-02-12.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: N/A
AEROSPACI score: 0.22 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Histone H3.1
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9za_
  • Chain 'B':
    Compound: histone h4
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9zb_
  • Chain 'C':
    Compound: Histone H2A type 1-B/E
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9zc_
  • Chain 'D':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BJ, H2BFR
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9zd_
  • Chain 'E':
    Compound: Histone H3.1
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9ze_
  • Chain 'F':
    Compound: histone h4
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9zf_
  • Chain 'G':
    Compound: Histone H2A type 1-B/E
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9zg_
  • Chain 'H':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BJ, H2BFR
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9zh_
  • Chain 'I':
    Compound: DNA (338-mer)
    Species: other sequences [TaxId:28384]
  • Chain 'J':
    Compound: DNA (338-mer)
    Species: other sequences [TaxId:28384]
  • Chain 'K':
    Compound: Histone H3.1
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9zk_
  • Chain 'L':
    Compound: histone h4
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9zl_
  • Chain 'M':
    Compound: Histone H2A type 1-B/E
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9zm_
  • Chain 'N':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BJ, H2BFR
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9zn_
  • Chain 'O':
    Compound: Histone H3.1
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9zo_
  • Chain 'P':
    Compound: histone h4
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9zp_
  • Chain 'Q':
    Compound: Histone H2A type 1-B/E
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9zq_
  • Chain 'R':
    Compound: Histone H2B type 1-J
    Species: Homo sapiens [TaxId:9606]
    Gene: HIST1H2BJ, H2BFR
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9zr_
  • Chain 'S':
    Compound: Histone H1x
    Species: Homo sapiens [TaxId:9606]
    Gene: H1FX
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6l9zs_
  • Heterogens: CL, CA, K, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6l9zA (A:)
martkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqkste
llirklpfqrlvreiaqdfktdlrfqssavmalqeaceaylvglfedtnlcaihakrvti
mpkdiqlarrirgera

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zA (A:)
phryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqeace
aylvglfedtnlcaihakrvtimpkdiqlarrirgera

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6l9zB (B:)
msgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlk
vflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zB (B:)
rkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakr
ktvtamdvvyalkrqgrtlygfgg

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6l9zC (C:)
msgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleylt
aeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpkk
teshhkakgk

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zC (C:)
arakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelagna
ardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpkkte

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >6l9zD (D:)
mpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgisskam
gimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavt
kytsak

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zD (D:)
krsrkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrsti
tsreiqtavrlllpgelakhavsegtkavtkytsak

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >6l9zE (E:)
martkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqkste
llirklpfqrlvreiaqdfktdlrfqssavmalqeaceaylvglfedtnlcaihakrvti
mpkdiqlarrirgera

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zE (E:)
kkphryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqea
ceaylvglfedtnlcaihakrvtimpkdiqlarrirgera

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >6l9zF (F:)
msgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlk
vflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zF (F:)
krhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtyteh
akrktvtamdvvyalkrqgrtlygfgg

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >6l9zG (G:)
msgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleylt
aeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpkk
teshhkakgk

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zG (G:)
kaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelagnaard
nkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpkk

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >6l9zH (H:)
mpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgisskam
gimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavt
kytsak

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zH (H:)
krsrkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrsti
tsreiqtavrlllpgelakhavsegtkavtkytsak

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    Sequence, based on SEQRES records: (download) 
    >6l9zK (K:)
martkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqkste
llirklpfqrlvreiaqdfktdlrfqssavmalqeaceaylvglfedtnlcaihakrvti
mpkdiqlarrirgera

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zK (K:)
kphryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqeac
eaylvglfedtnlcaihakrvtimpkdiqlarrirgera

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >6l9zL (L:)
msgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlk
vflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zL (L:)
hrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehak
rktvtamdvvyalkrqgrtlygfgg

  • Chain 'M':
    Sequence, based on SEQRES records: (download) 
    >6l9zM (M:)
msgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleylt
aeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpkk
teshhkakgk

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zM (M:)
rakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelagnaa
rdnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpkkte

  • Chain 'N':
    Sequence, based on SEQRES records: (download) 
    >6l9zN (N:)
mpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgisskam
gimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavt
kytsak

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zN (N:)
rkrsrkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrst
itsreiqtavrlllpgelakhavsegtkavtkytsak

  • Chain 'O':
    Sequence, based on SEQRES records: (download) 
    >6l9zO (O:)
martkqtarkstggkaprkqlatkaarksapatggvkkphryrpgtvalreirryqkste
llirklpfqrlvreiaqdfktdlrfqssavmalqeaceaylvglfedtnlcaihakrvti
mpkdiqlarrirgera

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zO (O:)
kkphryrpgtvalreirryqkstellirklpfqrlvreiaqdfktdlrfqssavmalqea
ceaylvglfedtnlcaihakrvtimpkdiqlarrirgera

  • Chain 'P':
    Sequence, based on SEQRES records: (download) 
    >6l9zP (P:)
msgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlk
vflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zP (P:)
glgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvird
avtytehakrktvtamdvvyalkrqgrtlygfgg

  • Chain 'Q':
    Sequence, based on SEQRES records: (download) 
    >6l9zQ (Q:)
msgrgkqggkarakaktrssraglqfpvgrvhrllrkgnyservgagapvylaavleylt
aeilelagnaardnkktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpkk
teshhkakgk

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zQ (Q:)
aktrssraglqfpvgrvhrllrkgnyservgagapvylaavleyltaeilelagnaardn
kktriiprhlqlairndeelnkllgrvtiaqggvlpniqavllpkk

  • Chain 'R':
    Sequence, based on SEQRES records: (download) 
    >6l9zR (R:)
mpepaksapapkkgskkavtkaqkkdgkkrkrsrkesysiyvykvlkqvhpdtgisskam
gimnsfvndiferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavt
kytsak

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zR (R:)
krsrkesysiyvykvlkqvhpdtgisskamgimnsfvndiferiageasrlahynkrsti
tsreiqtavrlllpgelakhavsegtkavtkytsak

  • Chain 'S':
    Sequence, based on SEQRES records: (download) 
    >6l9zS (S:)
msveleealpvttaegmakkvtkaggsaalspskkrknskkknqpgkysqlvvetirrlg
erngsslakiyteakkvpwfdqqngrtylkysikalvqndtllqvkgtgangsfklnrkk
legggerrgapaaatapaptahkakkaapgaagsrradkkpargqkpeqrshkkgagakk
dkggkakktaaaggkkvkkaakpsvpkvpkgrk

    Sequence, based on observed residues (ATOM records): (download) 
    >6l9zS (S:)
nskkknqpgkysqlvvetirrlgerngsslakiyteakkvpwfdqqngrtylkysikalv
qndtllqvkgtgangsfklnrkkl