PDB entry 4nid

View 4nid on RCSB PDB site
Description: Crystal structure of AlkB protein with cofactors bound to dsDNA containing m6A
Class: oxidoreductase/DNA
Keywords: DNA/RNA direct repair, jelly-roll fold, DNA/RNA demethylation repair, Fe(II), 2-KG, OXIDOREDUCTASE-DNA complex
Deposited on 2013-11-06, released 2014-04-16
The last revision prior to the SCOPe 2.08 freeze date was dated 2014-05-28, with a file datestamp of 2014-05-23.
Experiment type: XRAY
Resolution: 1.58 Å
R-factor: 0.179
AEROSPACI score: 0.52 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Alpha-ketoglutarate-dependent dioxygenase AlkB
    Species: Escherichia coli [TaxId:562]
    Gene: alkB, aidD, b2212, JW2200
    Database cross-references and differences (RAF-indexed):
    • Uniprot P05050 (0-End)
      • engineered mutation (117)
    Domains in SCOPe 2.08: d4nida_
  • Chain 'B':
    Compound: 5'-d(*tp*ap*gp*gp*tp*ap*ap*(6ma)p*ap*cp*cp*gp*t)-3'
  • Chain 'C':
    Compound: 5'-d(*ap*ap*cp*gp*gp*tp*ap*tp*tp*ap*cp*cp*t)-3'
  • Heterogens: MN, AKG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4nidA (A:)
    qeplaagavilrrfafnaaeqlirdindvasqspfrqmvtpggytmsvamtncghlgwtt
    hrqgylyspidpqtnkpwpampqsfhnlcqraataagypdfqpdaclinryapgaklclh
    qdkdepdlrapivsvslglpaifqfgglkrndplkrlllehgdvvvwggesrlfyhgiqp
    lkagfhpltidcrynltfrqagkke
    

    Sequence, based on observed residues (ATOM records): (download)
    >4nidA (A:)
    qeplaagavilrrfafnaaeqlirdindvasqspfrqmvtpggytmsvamtncghlgwtt
    hrqgylyspidpqtnkpwpampqsfhnlcqraataagypdfqpdaclinryapgaklclh
    qdkdepdlrapivsvslglpaifqfgglkrndplkrlllehgdvvvwggesrlfyhgiqp
    lkagfhpltidcrynltfrqagk
    

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    No sequence available.