PDB entry 6upu

View 6upu on RCSB PDB site
Description: Crystal structure of the Orientia tsutsugamushi OtDUB in complex with three molecules of ubiquitin
Class: hydrolase
Keywords: deubiquitylase, Orientia, CE clan, ubiquitin, HYDROLASE
Deposited on 2019-10-18, released 2020-04-01
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-04-14, with a file datestamp of 2021-04-09.
Experiment type: XRAY
Resolution: 2.2 Å
R-factor: N/A
AEROSPACI score: 0.33 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: ULP_PROTEASE domain-containing protein
    Species: Orientia tsutsugamushi (strain Ikeda) [TaxId:334380]
    Gene: OTT_1962
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed):
    • Uniprot F5H388 (3-78)
      • expression tag (2)
    Domains in SCOPe 2.08: d6upub1, d6upub2
  • Chain 'C':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6upuc_
  • Chain 'D':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6upud_
  • Chain 'E':
    Compound: ULP_PROTEASE domain-containing protein
    Species: Orientia tsutsugamushi (strain Ikeda) [TaxId:334380]
    Gene: OTT_1962
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed):
    • Uniprot F5H388 (3-78)
      • expression tag (2)
    Domains in SCOPe 2.08: d6upuf1, d6upuf2
  • Chain 'G':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6upug_
  • Chain 'H':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed):
    • Uniprot F5H388 (3-End)
      • expression tag (2)
    Domains in SCOPe 2.08: d6upuh1, d6upuh2
  • Chain 'I':
    Compound: ULP_PROTEASE domain-containing protein
    Species: Orientia tsutsugamushi (strain Ikeda) [TaxId:334380]
    Gene: OTT_1962
    Database cross-references and differences (RAF-indexed):
  • Chain 'J':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed):
    • Uniprot F5H388 (3-78)
      • expression tag (2)
    Domains in SCOPe 2.08: d6upuj1, d6upuj2
  • Chain 'K':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed):
    • Uniprot F5H388 (3-End)
      • expression tag (2)
    Domains in SCOPe 2.08: d6upuk1, d6upuk2
  • Chain 'L':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6upul_
  • Chain 'M':
    Compound: ULP_PROTEASE domain-containing protein
    Species: Orientia tsutsugamushi (strain Ikeda) [TaxId:334380]
    Gene: OTT_1962
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed):
    • Uniprot F5H388 (3-78)
      • expression tag (1-2)
    Domains in SCOPe 2.08: d6upun1, d6upun2
  • Chain 'O':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6upuo_
  • Chain 'P':
    Compound: Ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed):
    • Uniprot F5H388 (3-78)
      • expression tag (2)
    Domains in SCOPe 2.08: d6upup1, d6upup2
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6upuB (B:)
gggmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
dyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6upuB (B:)
gmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdy
niqkestlhlvlrlrgg

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6upuC (C:)
gggmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
dyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6upuC (C:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrgg

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >6upuD (D:)
gggmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
dyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6upuD (D:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrgg

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >6upuF (F:)
gggmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
dyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6upuF (F:)
gmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdy
niqkestlhlvlrlrgg

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >6upuG (G:)
gggmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
dyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6upuG (G:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrg

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >6upuH (H:)
gggmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
dyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6upuH (H:)
gmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdy
niqkestlhlvlrlrg

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >6upuJ (J:)
gggmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
dyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6upuJ (J:)
gmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdy
niqkestlhlvlrlrgg

  • Chain 'K':
    Sequence, based on SEQRES records: (download) 
    >6upuK (K:)
gggmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
dyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6upuK (K:)
gmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdy
niqkestlhlvlrlr

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >6upuL (L:)
gggmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
dyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6upuL (L:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrgg

  • Chain 'M':
    No sequence available.

  • Chain 'N':
    Sequence, based on SEQRES records: (download) 
    >6upuN (N:)
gggmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
dyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6upuN (N:)
ggmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsd
yniqkestlhlvlrlrgg

  • Chain 'O':
    Sequence, based on SEQRES records: (download) 
    >6upuO (O:)
gggmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
dyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6upuO (O:)
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyn
iqkestlhlvlrlrg

  • Chain 'P':
    Sequence, based on SEQRES records: (download) 
    >6upuP (P:)
gggmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtls
dyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6upuP (P:)
gmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdy
niqkestlhlvlrlrgg