PDB entry 3d0i

View 3d0i on RCSB PDB site
Description: Crystal structure of spike protein receptor-binding domain from the 2005-2006 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2
Class: hydrolase
Keywords: SARS coronavirus, spike protein, receptor-binding domain, RBD, angiotensin-converting enzyme 2, ACE2, virus-host interface, host adaptation, cross-species infections, human, palm civet, Carboxypeptidase, Chloride, Glycoprotein, Hydrolase, Membrane, Metal-binding, Metalloprotease, Protease, Secreted, Transmembrane, Envelope protein, Host-virus interaction, Lipoprotein, Palmitate, Virion, Virulence
Deposited on 2008-05-01, released 2008-07-08
The last revision prior to the SCOPe 2.01 freeze date was dated 2011-06-15, with a file datestamp of 2011-06-10.
Experiment type: XRAY
Resolution: 2.9 Å
R-factor: 0.227
AEROSPACI score: 0.23 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Angiotensin-converting enzyme 2
    Species: Paguma larvata, Homo sapiens
    Gene: ACE2
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3d0ia_
  • Chain 'B':
    Compound: Angiotensin-converting enzyme 2
    Species: Paguma larvata, Homo sapiens
    Gene: ACE2
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3d0ib_
  • Chain 'E':
    Compound: Spike protein S1
    Species: Human SARS coronavirus
    Gene: S
    Database cross-references and differences (RAF-indexed):
    • Uniprot P59594 (0-178)
      • conflict (155-156)
      • conflict (163)
    Domains in SCOPe 2.01: d3d0ie_
  • Chain 'F':
    Compound: Spike protein S1
    Species: Human SARS coronavirus
    Gene: S
    Database cross-references and differences (RAF-indexed):
    • Uniprot P59594 (0-178)
      • conflict (155-156)
      • conflict (163)
    Domains in SCOPe 2.01: d3d0if_
  • Heterogens: NDG, NAG, ZN, CL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3d0iA (A:)
    stteelaktfletfnyeaqelsyqssvaswnyntniteenvqnmnnagdkwsaflkeqst
    laqmyplqeiqnltvklqlqalqqngssvlsedkskrlntilntmstiystgkvcnpdnp
    qeclllepglneimansldynerlwaweswrsevgkqlrplyeeyvvlknemaranhyed
    ygdywrgdyevngvdgydysrgqliedvehtfeeikplyehlhayvraklmnaypsyisp
    igclpahllgdmwgrfwtnlysltvpfgqkpnidvtdamvdqawdaqrifkeaekffvsv
    glpnmtqgfwensmltdpgnvqkavchptawdlgkgdfrilmctkvtmddfltahhemgh
    iqydmayaaqpfllrnganegfheavgeimslsaatpkhlksigllspdfqedneteinf
    llkqaltivgtlpftymlekwrwmvfkgeipkdqwmkkwwemkreivgvvepvphdetyc
    dpaslfhvsndysfiryytrtlyqfqfqealcqaakhegplhkcdisnsteagqklfnml
    rlgksepwtlalenvvgaknmnvrpllnyfeplftwlkdqnknsfvgwstdwspyad
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3d0iB (B:)
    stteelaktfletfnyeaqelsyqssvaswnyntniteenvqnmnnagdkwsaflkeqst
    laqmyplqeiqnltvklqlqalqqngssvlsedkskrlntilntmstiystgkvcnpdnp
    qeclllepglneimansldynerlwaweswrsevgkqlrplyeeyvvlknemaranhyed
    ygdywrgdyevngvdgydysrgqliedvehtfeeikplyehlhayvraklmnaypsyisp
    igclpahllgdmwgrfwtnlysltvpfgqkpnidvtdamvdqawdaqrifkeaekffvsv
    glpnmtqgfwensmltdpgnvqkavchptawdlgkgdfrilmctkvtmddfltahhemgh
    iqydmayaaqpfllrnganegfheavgeimslsaatpkhlksigllspdfqedneteinf
    llkqaltivgtlpftymlekwrwmvfkgeipkdqwmkkwwemkreivgvvepvphdetyc
    dpaslfhvsndysfiryytrtlyqfqfqealcqaakhegplhkcdisnsteagqklfnml
    rlgksepwtlalenvvgaknmnvrpllnyfeplftwlkdqnknsfvgwstdwspyad
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3d0iE (E:)
    pfgevfnatkfpsvyawerkkisncvadysvlynstffstfkcygvsatklndlcfsnvy
    adsfvvkgddvrqiapgqtgviadynyklpddfmgcvlawntrnidatstgnynykyryl
    rhgklrpferdisnvpfspdgkpctppalncywplrgygfyttsgigyqpyrvvvlsfe
    

    Sequence, based on observed residues (ATOM records): (download)
    >3d0iE (E:)
    pfgevfnatkfpsvyawerkkisncvadysvlynstffstfkcygvsatklnvyadsfvv
    kgddvrqiapgqtgviadynyklpddfmgcvlawntrnidatstgnynykyrylrhgklr
    pferdisnvpfspdgkpctppalncywplrgygfyttsgigyqpyrvvvlsfe
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3d0iF (F:)
    pfgevfnatkfpsvyawerkkisncvadysvlynstffstfkcygvsatklndlcfsnvy
    adsfvvkgddvrqiapgqtgviadynyklpddfmgcvlawntrnidatstgnynykyryl
    rhgklrpferdisnvpfspdgkpctppalncywplrgygfyttsgigyqpyrvvvlsfe
    

    Sequence, based on observed residues (ATOM records): (download)
    >3d0iF (F:)
    pfgevfnatkfpsvyawerkkisncvadysvlynstffstfkcygvsatklnvyadsfvv
    kgddvrqiapgqtgviadynyklpddfmgcvlawntrnidatstgnynykyrylrhgklr
    pferdisnvpfspdgkpctppalncywplrgygfyttsgigyqpyrvvvlsfe