PDB entry 1ynf

View 1ynf on RCSB PDB site
Description: Crystal Structure of N-Succinylarginine Dihydrolase, AstB, bound to Substrate and Product, an Enzyme from the Arginine Catabolic Pathway of Escherichia coli
Class: hydrolase
Keywords: Succinylarginine, Dihydrolase
Deposited on 2005-01-24, released 2005-02-15
The last revision prior to the SCOPe 2.04 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 1.9 Å
R-factor: 0.214
AEROSPACI score: 0.43 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Succinylarginine Dihydrolase
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P76216 (12-End)
      • modified residue (59)
      • modified residue (116)
      • modified residue (201)
      • modified residue (295)
      • modified residue (327-328)
      • modified residue (367)
      • modified residue (395-396)
    Domains in SCOPe 2.04: d1ynfa1
  • Chain 'B':
    Compound: Succinylarginine Dihydrolase
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P76216 (12-End)
      • modified residue (59)
      • modified residue (116)
      • modified residue (201)
      • modified residue (295)
      • modified residue (327-328)
      • modified residue (367)
      • modified residue (395-396)
    Domains in SCOPe 2.04: d1ynfb_
  • Chain 'C':
    Compound: Succinylarginine Dihydrolase
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P76216 (12-End)
      • modified residue (59)
      • modified residue (116)
      • modified residue (201)
      • modified residue (295)
      • modified residue (327-328)
      • modified residue (367)
      • modified residue (395-396)
    Domains in SCOPe 2.04: d1ynfc_
  • Chain 'D':
    Compound: Succinylarginine Dihydrolase
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P76216 (12-End)
      • modified residue (59)
      • modified residue (116)
      • modified residue (201)
      • modified residue (295)
      • modified residue (327-328)
      • modified residue (367)
      • modified residue (395-396)
    Domains in SCOPe 2.04: d1ynfd_
  • Chain 'E':
    Compound: Succinylarginine Dihydrolase
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P76216 (12-End)
      • modified residue (59)
      • modified residue (116)
      • modified residue (201)
      • modified residue (295)
      • modified residue (327-328)
      • modified residue (367)
      • modified residue (395-396)
    Domains in SCOPe 2.04: d1ynfe_
  • Chain 'F':
    Compound: Succinylarginine Dihydrolase
    Species: Escherichia coli [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P76216 (12-End)
      • modified residue (59)
      • modified residue (116)
      • modified residue (201)
      • modified residue (295)
      • modified residue (327-328)
      • modified residue (367)
      • modified residue (395-396)
    Domains in SCOPe 2.04: d1ynff_
  • Heterogens: K, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >1ynfA (A:)
    mgsshhhhhhgsnawevnfdglvglthhyaglsfgneastrhrfqvsnprlaakqgllkm
    kaladagfpqavippherpfipvlrqlgfsgsdeqvlekvarqaphwlssvssaspmwva
    naatiapsadtldgkvhltvanlnnkfhrsleapvtesllkaifndeekfsvhsalpqva
    llgdegaanhnrlgghygepgmqlfvygreegndtrpsryparqtreaseavarlnqvnp
    qqvifaqqnpdvidqgvfhndviavsnrqvlfchqqafarqsqllanlrarvngfmaiev
    patqvsvsdtvstylfnsqllsrddgsmmlvlpqecrehagvwgylnellaadnpiselk
    vfdlresmangggpaclrlrvvlteeerravnpavmmndtlfnalndwvdryyrdrltaa
    dladpqllregrealdvlsqllnlgsvypfqregggng
    

    Sequence, based on observed residues (ATOM records): (download)
    >1ynfA (A:)
    nawevnfdglvglthhyahrfqvsnprlaakqgllkmkaladagfpqavippherpfipv
    lrqlgfsgsdeqvlekvarqaphwlssvssaspmwvanaatiapsadtldgkvhltvanl
    nnkfhrsleapvtesllkaifndeekfsvhsalpqvallgdegaanhnrlgghygepgmq
    lfvygreegndtrpsryparqtreaseavarlnqvnpqqvifaqqnpdvidqgvfhndvi
    avsnrqvlfchqqafarqsqllanlrarvngfmaievpatqvsvsdtvstylfnsqllsr
    ddgsmmlvlpqecrehagvwgylnellaadnpiselkvfdlresmangggpaclrlrvvl
    teeerravnpavmmndtlfnalndwvdryyrdrltaadladpqllregrealdvlsqlln
    lgsvypfqr
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >1ynfB (B:)
    mgsshhhhhhgsnawevnfdglvglthhyaglsfgneastrhrfqvsnprlaakqgllkm
    kaladagfpqavippherpfipvlrqlgfsgsdeqvlekvarqaphwlssvssaspmwva
    naatiapsadtldgkvhltvanlnnkfhrsleapvtesllkaifndeekfsvhsalpqva
    llgdegaanhnrlgghygepgmqlfvygreegndtrpsryparqtreaseavarlnqvnp
    qqvifaqqnpdvidqgvfhndviavsnrqvlfchqqafarqsqllanlrarvngfmaiev
    patqvsvsdtvstylfnsqllsrddgsmmlvlpqecrehagvwgylnellaadnpiselk
    vfdlresmangggpaclrlrvvlteeerravnpavmmndtlfnalndwvdryyrdrltaa
    dladpqllregrealdvlsqllnlgsvypfqregggng
    

    Sequence, based on observed residues (ATOM records): (download)
    >1ynfB (B:)
    nawevnfdglvglthhyahrfqvsnprlaakqgllkmkaladagfpqavippherpfipv
    lrqlgfsgsdeqvlekvarqaphwlssvssaspmwvanaatiapsadtldgkvhltvanl
    nnkfhrsleapvtesllkaifndeekfsvhsalpqvallgdegaanhnrlgghygepgmq
    lfvygreegndtrpsryparqtreaseavarlnqvnpqqvifaqqnpdvidqgvfhndvi
    avsnrqvlfchqqafarqsqllanlrarvngfmaievpatqvsvsdtvstylfnsqllsr
    ddgsmmlvlpqecrehagvwgylnellaadnpiselkvfdlresmangggpaclrlrvvl
    teeerravnpavmmndtlfnalndwvdryyrdrltaadladpqllregrealdvlsqlln
    lgsvypfqr
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >1ynfC (C:)
    mgsshhhhhhgsnawevnfdglvglthhyaglsfgneastrhrfqvsnprlaakqgllkm
    kaladagfpqavippherpfipvlrqlgfsgsdeqvlekvarqaphwlssvssaspmwva
    naatiapsadtldgkvhltvanlnnkfhrsleapvtesllkaifndeekfsvhsalpqva
    llgdegaanhnrlgghygepgmqlfvygreegndtrpsryparqtreaseavarlnqvnp
    qqvifaqqnpdvidqgvfhndviavsnrqvlfchqqafarqsqllanlrarvngfmaiev
    patqvsvsdtvstylfnsqllsrddgsmmlvlpqecrehagvwgylnellaadnpiselk
    vfdlresmangggpaclrlrvvlteeerravnpavmmndtlfnalndwvdryyrdrltaa
    dladpqllregrealdvlsqllnlgsvypfqregggng
    

    Sequence, based on observed residues (ATOM records): (download)
    >1ynfC (C:)
    nawevnfdglvglthhyahrfqvsnprlaakqgllkmkaladagfpqavippherpfipv
    lrqlgfsgsdeqvlekvarqaphwlssvssaspmwvanaatiapsadtldgkvhltvanl
    nnkfhrsleapvtesllkaifndeekfsvhsalpqvallgdegaanhnrlgghygepgmq
    lfvygreegndtrpsryparqtreaseavarlnqvnpqqvifaqqnpdvidqgvfhndvi
    avsnrqvlfchqqafarqsqllanlrarvngfmaievpatqvsvsdtvstylfnsqllsr
    ddgsmmlvlpqecrehagvwgylnellaadnpiselkvfdlresmangggpaclrlrvvl
    teeerravnpavmmndtlfnalndwvdryyrdrltaadladpqllregrealdvlsqlln
    lgsvypfqr
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >1ynfD (D:)
    mgsshhhhhhgsnawevnfdglvglthhyaglsfgneastrhrfqvsnprlaakqgllkm
    kaladagfpqavippherpfipvlrqlgfsgsdeqvlekvarqaphwlssvssaspmwva
    naatiapsadtldgkvhltvanlnnkfhrsleapvtesllkaifndeekfsvhsalpqva
    llgdegaanhnrlgghygepgmqlfvygreegndtrpsryparqtreaseavarlnqvnp
    qqvifaqqnpdvidqgvfhndviavsnrqvlfchqqafarqsqllanlrarvngfmaiev
    patqvsvsdtvstylfnsqllsrddgsmmlvlpqecrehagvwgylnellaadnpiselk
    vfdlresmangggpaclrlrvvlteeerravnpavmmndtlfnalndwvdryyrdrltaa
    dladpqllregrealdvlsqllnlgsvypfqregggng
    

    Sequence, based on observed residues (ATOM records): (download)
    >1ynfD (D:)
    nawevnfdglvglthhyahrfqvsnprlaakqgllkmkaladagfpqavippherpfipv
    lrqlgfsgsdeqvlekvarqaphwlssvssaspmwvanaatiapsadtldgkvhltvanl
    nnkfhrsleapvtesllkaifndeekfsvhsalpqvallgdegaanhnrlgghygepgmq
    lfvygreegndtrpsryparqtreaseavarlnqvnpqqvifaqqnpdvidqgvfhndvi
    avsnrqvlfchqqafarqsqllanlrarvngfmaievpatqvsvsdtvstylfnsqllsr
    ddgsmmlvlpqecrehagvwgylnellaadnpiselkvfdlresmangggpaclrlrvvl
    teeerravnpavmmndtlfnalndwvdryyrdrltaadladpqllregrealdvlsqlln
    lgsvypfqr
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >1ynfE (E:)
    mgsshhhhhhgsnawevnfdglvglthhyaglsfgneastrhrfqvsnprlaakqgllkm
    kaladagfpqavippherpfipvlrqlgfsgsdeqvlekvarqaphwlssvssaspmwva
    naatiapsadtldgkvhltvanlnnkfhrsleapvtesllkaifndeekfsvhsalpqva
    llgdegaanhnrlgghygepgmqlfvygreegndtrpsryparqtreaseavarlnqvnp
    qqvifaqqnpdvidqgvfhndviavsnrqvlfchqqafarqsqllanlrarvngfmaiev
    patqvsvsdtvstylfnsqllsrddgsmmlvlpqecrehagvwgylnellaadnpiselk
    vfdlresmangggpaclrlrvvlteeerravnpavmmndtlfnalndwvdryyrdrltaa
    dladpqllregrealdvlsqllnlgsvypfqregggng
    

    Sequence, based on observed residues (ATOM records): (download)
    >1ynfE (E:)
    nawevnfdglvglthhyahrfqvsnprlaakqgllkmkaladagfpqavippherpfipv
    lrqlgfsgsdeqvlekvarqaphwlssvssaspmwvanaatiapsadtldgkvhltvanl
    nnkfhrsleapvtesllkaifndeekfsvhsalpqvallgdegaanhnrlgghygepgmq
    lfvygreegndtrpsryparqtreaseavarlnqvnpqqvifaqqnpdvidqgvfhndvi
    avsnrqvlfchqqafarqsqllanlrarvngfmaievpatqvsvsdtvstylfnsqllsr
    ddgsmmlvlpqecrehagvwgylnellaadnpiselkvfdlresmangggpaclrlrvvl
    teeerravnpavmmndtlfnalndwvdryyrdrltaadladpqllregrealdvlsqlln
    lgsvypfqr
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >1ynfF (F:)
    mgsshhhhhhgsnawevnfdglvglthhyaglsfgneastrhrfqvsnprlaakqgllkm
    kaladagfpqavippherpfipvlrqlgfsgsdeqvlekvarqaphwlssvssaspmwva
    naatiapsadtldgkvhltvanlnnkfhrsleapvtesllkaifndeekfsvhsalpqva
    llgdegaanhnrlgghygepgmqlfvygreegndtrpsryparqtreaseavarlnqvnp
    qqvifaqqnpdvidqgvfhndviavsnrqvlfchqqafarqsqllanlrarvngfmaiev
    patqvsvsdtvstylfnsqllsrddgsmmlvlpqecrehagvwgylnellaadnpiselk
    vfdlresmangggpaclrlrvvlteeerravnpavmmndtlfnalndwvdryyrdrltaa
    dladpqllregrealdvlsqllnlgsvypfqregggng
    

    Sequence, based on observed residues (ATOM records): (download)
    >1ynfF (F:)
    nawevnfdglvglthhyahrfqvsnprlaakqgllkmkaladagfpqavippherpfipv
    lrqlgfsgsdeqvlekvarqaphwlssvssaspmwvanaatiapsadtldgkvhltvanl
    nnkfhrsleapvtesllkaifndeekfsvhsalpqvallgdegaanhnrlgghygepgmq
    lfvygreegndtrpsryparqtreaseavarlnqvnpqqvifaqqnpdvidqgvfhndvi
    avsnrqvlfchqqafarqsqllanlrarvngfmaievpatqvsvsdtvstylfnsqllsr
    ddgsmmlvlpqecrehagvwgylnellaadnpiselkvfdlresmangggpaclrlrvvl
    teeerravnpavmmndtlfnalndwvdryyrdrltaadladpqllregrealdvlsqlln
    lgsvypfqr