PDB entry 5omx

View 5omx on RCSB PDB site
Description: X-ray Structure of the H2A-N38C Nucleosome Core Particle
Class: DNA binding protein
Keywords: nucleosome core particle, histone, DNA, DNA binding protein
Deposited on 2017-08-02, released 2017-11-15
The last revision prior to the SCOPe 2.06 freeze date was dated 2017-11-15, with a file datestamp of 2017-11-10.
Experiment type: XRAY
Resolution: 2.32 Å
R-factor: N/A
AEROSPACI score: 0.25 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Histone H3.2
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P84233
      • conflict (101)
      • engineered mutation (109)
  • Chain 'B':
    Compound: histone h4
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5omxb_
  • Chain 'C':
    Compound: histone h2a
    Species: Xenopus laevis [TaxId:8355]
    Gene: hist1h2aj, LOC494591
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q6AZJ8
      • engineered mutation (37)
    Domains in SCOPe 2.06: d5omxc_
  • Chain 'D':
    Compound: Histone H2B 1.1
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P02281 (Start-121)
      • conflict (28)
    Domains in SCOPe 2.06: d5omxd_
  • Chain 'E':
    Compound: Histone H3.2
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P84233 (Start-134)
      • conflict (101)
      • engineered mutation (109)
  • Chain 'F':
    Compound: histone h4
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5omxf_
  • Chain 'G':
    Compound: histone h2a
    Species: Xenopus laevis [TaxId:8355]
    Gene: hist1h2aj, LOC494591
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q6AZJ8
      • engineered mutation (37)
    Domains in SCOPe 2.06: d5omxg_
  • Chain 'H':
    Compound: Histone H2B 1.1
    Species: Xenopus laevis [TaxId:8355]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P02281
      • conflict (28)
    Domains in SCOPe 2.06: d5omxh_
  • Chain 'I':
    Compound: DNA (147-mer)
    Species: Homo sapiens [TaxId:9606]
    Gene: alpha satellite
  • Chain 'J':
    Compound: DNA (147-mer)
    Species: Homo sapiens [TaxId:9606]
  • Heterogens: MN, CL, HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5omxB (B:)
    msgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlk
    vflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >5omxB (B:)
    dniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtytehakrktvta
    mdvvyalkrqgrtlygfgg
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5omxC (C:)
    sgrgkqggktrakaktrssraglqfpvgrvhrllrkgcyaervgagapvylaavleylta
    eilelagnaardnkktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpkkt
    essksaksk
    

    Sequence, based on observed residues (ATOM records): (download)
    >5omxC (C:)
    aktrssraglqfpvgrvhrllrkgcyaervgagapvylaavleyltaeilelagnaardn
    kktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpk
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5omxD (D:)
    aksapapkkgskkavtktqkkdgkkrrktrkesyaiyvykvlkqvhpdtgisskamsimn
    sfvndvferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavtkyts
    ak
    

    Sequence, based on observed residues (ATOM records): (download)
    >5omxD (D:)
    trkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrstits
    reiqtavrlllpgelakhavsegtkavtkytsak
    

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >5omxF (F:)
    msgrgkggkglgkggakrhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlk
    vflenvirdavtytehakrktvtamdvvyalkrqgrtlygfgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >5omxF (F:)
    rhrkvlrdniqgitkpairrlarrggvkrisgliyeetrgvlkvflenvirdavtyteha
    krktvtamdvvyalkrqgrtlygfgg
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >5omxG (G:)
    sgrgkqggktrakaktrssraglqfpvgrvhrllrkgcyaervgagapvylaavleylta
    eilelagnaardnkktriiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpkkt
    essksaksk
    

    Sequence, based on observed residues (ATOM records): (download)
    >5omxG (G:)
    trssraglqfpvgrvhrllrkgcyaervgagapvylaavleyltaeilelagnaardnkk
    triiprhlqlavrndeelnkllgrvtiaqggvlpniqsvllpk
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >5omxH (H:)
    aksapapkkgskkavtktqkkdgkkrrktrkesyaiyvykvlkqvhpdtgisskamsimn
    sfvndvferiageasrlahynkrstitsreiqtavrlllpgelakhavsegtkavtkyts
    ak
    

    Sequence, based on observed residues (ATOM records): (download)
    >5omxH (H:)
    rktrkesyaiyvykvlkqvhpdtgisskamsimnsfvndvferiageasrlahynkrsti
    tsreiqtavrlllpgelakhavsegtkavtkytsa
    

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.