PDB entry 1yfj

View 1yfj on RCSB PDB site
Description: T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact
Class: transferase/DNA
Keywords: t4dam, methyltransferase, DNA, protein-DNA complex, transferase-DNA complex
Deposited on 2005-01-02, released 2005-05-17
The last revision prior to the SCOPe 2.08 freeze date was dated 2018-01-31, with a file datestamp of 2018-01-26.
Experiment type: XRAY
Resolution: 2.69 Å
R-factor: N/A
AEROSPACI score: 0.17 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '0':
    Compound: 5'-d(*tp*cp*ap*cp*ap*gp*gp*ap*tp*cp*cp*tp*gp*tp*g)-3'
    Species: synthetic, synthetic
  • Chain '1':
    Compound: 5'-d(*tp*cp*ap*cp*ap*gp*gp*ap*tp*cp*cp*tp*gp*tp*g)-3'
    Species: synthetic, synthetic
  • Chain '2':
    Compound: 5'-d(*tp*cp*ap*cp*ap*gp*gp*ap*tp*cp*cp*tp*gp*tp*g)-3'
    Species: synthetic, synthetic
  • Chain '3':
    Compound: 5'-d(*tp*cp*ap*cp*ap*gp*gp*ap*tp*cp*cp*tp*gp*tp*g)-3'
    Species: synthetic, synthetic
  • Chain '4':
    Compound: 5'-d(*tp*cp*ap*cp*ap*gp*gp*ap*tp*cp*cp*tp*gp*tp*g)-3'
    Species: synthetic, synthetic
  • Chain '5':
    Compound: 5'-d(*tp*cp*ap*cp*ap*gp*gp*ap*tp*cp*cp*tp*gp*tp*g)-3'
    Species: synthetic, synthetic
  • Chain '6':
    Compound: 5'-d(*tp*cp*ap*cp*ap*gp*gp*ap*tp*cp*cp*tp*gp*tp*g)-3'
    Species: synthetic, synthetic
  • Chain '7':
    Compound: 5'-d(*tp*cp*ap*cp*ap*gp*gp*ap*tp*cp*cp*tp*gp*tp*g)-3'
    Species: synthetic, synthetic
  • Chain '8':
    Compound: 5'-d(*tp*cp*ap*cp*ap*gp*gp*ap*tp*cp*cp*tp*gp*tp*g)-3'
    Species: synthetic, synthetic
  • Chain '9':
    Compound: 5'-d(*tp*cp*ap*cp*ap*gp*gp*ap*tp*cp*cp*tp*gp*tp*g)-3'
    Species: synthetic, synthetic
  • Chain 'A':
    Compound: DNA adenine methylase
    Species: Enterobacteria phage T4 sensu lato [TaxId:10665]
    Gene: dam
    Database cross-references and differences (RAF-indexed):
    • Uniprot P04392 (0-258)
      • see remark 999 (138-139)
      • see remark 999 (208)
    Domains in SCOPe 2.08: d1yfja1
  • Chain 'B':
    Compound: DNA adenine methylase
    Species: Enterobacteria phage T4 sensu lato [TaxId:10665]
    Gene: dam
    Database cross-references and differences (RAF-indexed):
    • Uniprot P04392 (0-258)
      • see remark 999 (138-139)
      • see remark 999 (208)
    Domains in SCOPe 2.08: d1yfjb_
  • Chain 'C':
    Compound: DNA adenine methylase
    Species: Enterobacteria phage T4 sensu lato [TaxId:10665]
    Gene: dam
    Database cross-references and differences (RAF-indexed):
    • Uniprot P04392 (0-258)
      • see remark 999 (138-139)
      • see remark 999 (208)
    Domains in SCOPe 2.08: d1yfjc_
  • Chain 'D':
    Compound: DNA adenine methylase
    Species: Enterobacteria phage T4 sensu lato [TaxId:10665]
    Gene: dam
    Database cross-references and differences (RAF-indexed):
    • Uniprot P04392 (0-258)
      • see remark 999 (138-139)
      • see remark 999 (208)
    Domains in SCOPe 2.08: d1yfjd_
  • Chain 'E':
    Compound: DNA adenine methylase
    Species: Enterobacteria phage T4 sensu lato [TaxId:10665]
    Gene: dam
    Database cross-references and differences (RAF-indexed):
    • Uniprot P04392 (0-258)
      • see remark 999 (138-139)
      • see remark 999 (208)
    Domains in SCOPe 2.08: d1yfje_
  • Chain 'F':
    Compound: DNA adenine methylase
    Species: Enterobacteria phage T4 sensu lato [TaxId:10665]
    Gene: dam
    Database cross-references and differences (RAF-indexed):
    • Uniprot P04392 (0-258)
      • see remark 999 (138-139)
      • see remark 999 (208)
    Domains in SCOPe 2.08: d1yfjf_
  • Heterogens: CL, CA, SAH, HOH

PDB Chain Sequences:

  • Chain '0':
    No sequence available.

  • Chain '1':
    No sequence available.

  • Chain '2':
    No sequence available.

  • Chain '3':
    No sequence available.

  • Chain '4':
    No sequence available.

  • Chain '5':
    No sequence available.

  • Chain '6':
    No sequence available.

  • Chain '7':
    No sequence available.

  • Chain '8':
    No sequence available.

  • Chain '9':
    No sequence available.

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1yfjA (A:)
mlgaiaytgnkqsllpelkshfpkynrfvdlfcgglsvslnvngpvlandiqepiiemyk
rlinvswddvlkvikqyklsktskeeflklredynktrdplllyvlhfhgfsnmirindk
gnfttpfgkrtinknsekrfnhfkqncdkiifsslhfkdvkildgdfvyvdppylitvad
ynkfwsedeekdllnlldslndrgikfglsnvlehhgkentllkewskkynvkhlnkkyv
fniyhskekngtdevyifn

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1yfjB (B:)
mlgaiaytgnkqsllpelkshfpkynrfvdlfcgglsvslnvngpvlandiqepiiemyk
rlinvswddvlkvikqyklsktskeeflklredynktrdplllyvlhfhgfsnmirindk
gnfttpfgkrtinknsekrfnhfkqncdkiifsslhfkdvkildgdfvyvdppylitvad
ynkfwsedeekdllnlldslndrgikfglsnvlehhgkentllkewskkynvkhlnkkyv
fniyhskekngtdevyifn

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1yfjC (C:)
mlgaiaytgnkqsllpelkshfpkynrfvdlfcgglsvslnvngpvlandiqepiiemyk
rlinvswddvlkvikqyklsktskeeflklredynktrdplllyvlhfhgfsnmirindk
gnfttpfgkrtinknsekrfnhfkqncdkiifsslhfkdvkildgdfvyvdppylitvad
ynkfwsedeekdllnlldslndrgikfglsnvlehhgkentllkewskkynvkhlnkkyv
fniyhskekngtdevyifn

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >1yfjD (D:)
mlgaiaytgnkqsllpelkshfpkynrfvdlfcgglsvslnvngpvlandiqepiiemyk
rlinvswddvlkvikqyklsktskeeflklredynktrdplllyvlhfhgfsnmirindk
gnfttpfgkrtinknsekrfnhfkqncdkiifsslhfkdvkildgdfvyvdppylitvad
ynkfwsedeekdllnlldslndrgikfglsnvlehhgkentllkewskkynvkhlnkkyv
fniyhskekngtdevyifn

    Sequence, based on observed residues (ATOM records): (download) 
    >1yfjD (D:)
mlgaiaytgnkqsllpelkshfpkynrfvdlfcgglsvslnvngpvlandiqepiiemyk
rlinvswddvlkvikqyklsktskeeflklredynktrdplllyvlhfhgfsnmirindk
gnfttpfgkrtinknsekrfnhfkqncdkiifsslhfkdvkildgdfvyvdppylitvad
ynkfwsedeekdllnlldslndrgikfglsnvlehhgkentllkewskkynvkhlnkkyv
fniyngtdevyifn

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >1yfjE (E:)
mlgaiaytgnkqsllpelkshfpkynrfvdlfcgglsvslnvngpvlandiqepiiemyk
rlinvswddvlkvikqyklsktskeeflklredynktrdplllyvlhfhgfsnmirindk
gnfttpfgkrtinknsekrfnhfkqncdkiifsslhfkdvkildgdfvyvdppylitvad
ynkfwsedeekdllnlldslndrgikfglsnvlehhgkentllkewskkynvkhlnkkyv
fniyhskekngtdevyifn

    Sequence, based on observed residues (ATOM records): (download) 
    >1yfjE (E:)
mlgaiaytgnkqsllpelkshfpkynrfvdlfcgglsvslnvngpvlandiqepiiemyk
rlinvswddvlkvikqyklsktskeeflklredynktrdplllyvlhfhgfsnmirindk
gnfttpfgkrtinknsekrfnhfkqncdkiifsslhfkdvkildgdfvyvdppylitvad
ynkfwsedeekdllnlldslndrgikfglsnvlehhgkentllkewskkynvkhltdevy
ifn

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >1yfjF (F:)
mlgaiaytgnkqsllpelkshfpkynrfvdlfcgglsvslnvngpvlandiqepiiemyk
rlinvswddvlkvikqyklsktskeeflklredynktrdplllyvlhfhgfsnmirindk
gnfttpfgkrtinknsekrfnhfkqncdkiifsslhfkdvkildgdfvyvdppylitvad
ynkfwsedeekdllnlldslndrgikfglsnvlehhgkentllkewskkynvkhlnkkyv
fniyhskekngtdevyifn

    Sequence, based on observed residues (ATOM records): (download) 
    >1yfjF (F:)
mlgaiaytgnkqsllpelkshfpkynrfvdlfcgglsvslnvngpvlandiqepiiemyk
rlinvswddvlkvikqyklsktskeeflklredynktrdplllyvlhfhgfsnmirindk
gnfttpfgkrtinknsekrfnhfkqncdkiifsslhfkdvkildgdfvyvdppylitvad
ynkfwsedeekdllnlldslndrgikfglsnvlehhgkentllkewskkynvkhltdevy
ifn