PDB entry 1nbf

View 1nbf on RCSB PDB site
Description: Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde
Class: hydrolase
Keywords: deubiquitinating enzyme, HAUSP, Ubiquitin binding, catalytic mechanisms of UPBs
Deposited on 2002-12-02, released 2003-01-07
The last revision prior to the SCOP 1.73 freeze date was dated 2003-01-07, with a file datestamp of 2007-06-04.
Experiment type: XRAY
Resolution: 2.3 Å
R-factor: 0.218
AEROSPACI score: 0.33 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Ubiquitin carboxyl-terminal hydrolase 7
    Species: HOMO SAPIENS
    Gene: USP7
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.73: d1nbfa_
  • Chain 'B':
    Compound: Ubiquitin carboxyl-terminal hydrolase 7
    Species: HOMO SAPIENS
    Gene: USP7
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.73: d1nbfb_
  • Chain 'C':
    Compound: Ubiquitin aldehyde
    Species: HOMO SAPIENS
    Gene: UBA52
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62988 (0-75)
      • modified residue (75)
    Domains in SCOP 1.73: d1nbfc_
  • Chain 'D':
    Compound: Ubiquitin aldehyde
    Species: HOMO SAPIENS
    Gene: UBA52
    Database cross-references and differences (RAF-indexed):
    • Uniprot P62988 (0-75)
      • modified residue (75)
    Domains in SCOP 1.73: d1nbfd_
  • Chain 'E':
    Compound: Ubiquitin carboxyl-terminal hydrolase 7
    Species: HOMO SAPIENS
    Gene: USP7
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.73: d1nbfe_
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >1nbfA (A:)
    kkhtgyvglknqgatcymnsllqtlfftnqlrkavymmptegddssksvplalqrvfyel
    qhsdkpvgtkkltksfgwetldsfmqhdvqelcrvlldnvenkmkgtcvegtipklfrgk
    mvsyiqckevdyrsdrredyydiqlsikgkknifesfvdyvaveqldgdnkydagehglq
    eaekgvkfltlppvlhlqlmrfmydpqtdqnikindrfefpeqlpldeflqktdpkdpan
    yilhavlvhsgdnhgghyvvylnpkgdgkwckfdddvvsrctkeeaiehnygghdddlsv
    rhctnaymlvyiresklsevlqavtdhdipqqlverlqeekrieaqkrkerqe
    

    Sequence, based on observed residues (ATOM records): (download)
    >1nbfA (A:)
    kkhtgyvglknqgatcymnsllqtlfftnqlrkavymmptegddssksvplalqrvfyel
    qhsdkpvgtkkltksfgwetldsfmqhdvqelcrvlldnvenkmkgtcvegtipklfrgk
    mvsyiqckevdyrsdrredyydiqlsikgkknifesfvdyvaveqldgdnkydagehglq
    eaekgvkfltlppvlhlqlmrfmydpqtdqnikindrfefpeqlpldeflqktdpkdpan
    yilhavlvhsgdnhgghyvvylnpkgdgkwckfdddvvsrctkeeaiehnygghdddlsv
    rhctnaymlvyiresklsevlqavtdhdipqqlverlqeekrieaqk
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >1nbfB (B:)
    kkhtgyvglknqgatcymnsllqtlfftnqlrkavymmptegddssksvplalqrvfyel
    qhsdkpvgtkkltksfgwetldsfmqhdvqelcrvlldnvenkmkgtcvegtipklfrgk
    mvsyiqckevdyrsdrredyydiqlsikgkknifesfvdyvaveqldgdnkydagehglq
    eaekgvkfltlppvlhlqlmrfmydpqtdqnikindrfefpeqlpldeflqktdpkdpan
    yilhavlvhsgdnhgghyvvylnpkgdgkwckfdddvvsrctkeeaiehnygghdddlsv
    rhctnaymlvyiresklsevlqavtdhdipqqlverlqeekrieaqkrkerqe
    

    Sequence, based on observed residues (ATOM records): (download)
    >1nbfB (B:)
    kkhtgyvglknqgatcymnsllqtlfftnqlrkavymmptegddssksvplalqrvfyel
    qhsdkpvgtkkltksfgwetldsfmqhdvqelcrvlldnvenkmkgtcvegtipklfrgk
    mvsyiqckevdyrsdrredyydiqlsikgkknifesfvdyvaveqldgdnkydagehglq
    eaekgvkfltlppvlhlqlmrfmydpqtdqnikindrfefpeqlpldeflqktdpkdpan
    yilhavlvhsgdnhgghyvvylnpkgdgkwckfdddvvsrctkeeaiehnygghdddlsv
    rhctnaymlvyiresklsevlqavtdhdipqqlverlqeekrieaqk
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1nbfC (C:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrlrgg
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download)
    >1nbfD (D:)
    mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
    iqkestlhlvlrlrgg
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >1nbfE (E:)
    kkhtgyvglknqgatcymnsllqtlfftnqlrkavymmptegddssksvplalqrvfyel
    qhsdkpvgtkkltksfgwetldsfmqhdvqelcrvlldnvenkmkgtcvegtipklfrgk
    mvsyiqckevdyrsdrredyydiqlsikgkknifesfvdyvaveqldgdnkydagehglq
    eaekgvkfltlppvlhlqlmrfmydpqtdqnikindrfefpeqlpldeflqktdpkdpan
    yilhavlvhsgdnhgghyvvylnpkgdgkwckfdddvvsrctkeeaiehnygghdddlsv
    rhctnaymlvyiresklsevlqavtdhdipqqlverlqeekrieaqkrkerqe
    

    Sequence, based on observed residues (ATOM records): (download)
    >1nbfE (E:)
    kkhtgyvglknqgatcymnsllqtlfftnqlrkavymmptegddssksvplalqrvfyel
    qhsdkpvgtkkltksfgwetldsfmqhdvqelcrvlldnvenkmkgtcvegtipklfrgk
    mvsyiqckevdyrsdrredyydiqlsikgkknifesfvdyvaveqldgdnkydagehglq
    eaekgvkfltlppvlhlqlmrfmnikindrfefpeqlpldeflqktdpkdpanyilhavl
    vhsgdnhgghyvvylnpkgdgkwckfdddvvsrctkeeaiehnygghdddlsvrhctnay
    mlvyiresklsevlqavtdhdipqqlverlqeekrieaqk