PDB entry 6njd

View 6njd on RCSB PDB site
Description: Crystal structure of RavD (residues 1-200) from Legionella pneumophila (strain Corby) complexed with Met-1 linked di-ubiquitin
Class: hydrolase
Keywords: Deubiquitinase, Bacterial effector, HYDROLASE
Deposited on 2019-01-03, released 2019-05-22
The last revision prior to the SCOPe 2.07 freeze date was dated 2019-05-22, with a file datestamp of 2019-05-17.
Experiment type: XRAY
Resolution: 2.05 Å
R-factor: N/A
AEROSPACI score: 0.3 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: di-ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed):
    • Uniprot F5H747 (5-End)
      • expression tag (0-4)
      • engineered mutation (79-80)
    Domains in SCOPe 2.07: d6njda1, d6njda2, d6njda3
  • Chain 'B':
    Compound: RavD
    Species: Legionella pneumophila [TaxId:446]
    Gene: LPC_0242
    Database cross-references and differences (RAF-indexed):
    • PDB 6NJD
  • Chain 'C':
    Compound: di-ubiquitin
    Species: Homo sapiens [TaxId:9606]
    Gene: UBC
    Database cross-references and differences (RAF-indexed):
    • Uniprot F5H747 (5-End)
      • engineered mutation (79-80)
    Domains in SCOPe 2.07: d6njdc1, d6njdc2
  • Chain 'D':
    Compound: RavD
    Species: Legionella pneumophila [TaxId:446]
    Gene: LPC_0242
    Database cross-references and differences (RAF-indexed):
    • PDB 6NJD
  • Heterogens: MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6njdA (A:)
gplgsmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrt
lsdyniqkestlhlvlrlrssmqifvktltgktitlevepsdtienvkakiqdkegippd
qqrlifagkqledgrtlsdyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6njdA (A:)
gplgsmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrt
lsdyniqkestlhlvlrlrssmqifvktltgktitlevepsdtienvkakiqdkegippd
qqrlifagkqledgrtlsdyniqkestlhlvlr

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6njdC (C:)
gplgsmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqledgrt
lsdyniqkestlhlvlrlrssmqifvktltgktitlevepsdtienvkakiqdkegippd
qqrlifagkqledgrtlsdyniqkestlhlvlrlrgg

    Sequence, based on observed residues (ATOM records): (download) 
    >6njdC (C:)
mqvktltgkttlvepsdtienvkakiqdkegippdqqrlifagkqledgrtlsdyniqtl
hlvlrlrssmqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkqle
dgrtlsdyniqkestlhlvlr

  • Chain 'D':
    No sequence available.