PDB entry 5ded

View 5ded on RCSB PDB site
Description: Crystal structure of the small alarmone synthethase 1 from Bacillus subtilis bound to its product pppGpp
Class: transferase
Keywords: (p)ppGpp, alarmone, stringent response, allosteric regulator, transferase
Deposited on 2015-08-25, released 2015-10-28
The last revision prior to the SCOPe 2.08 freeze date was dated 2015-11-04, with a file datestamp of 2015-10-30.
Experiment type: XRAY
Resolution: 2.94 Å
R-factor: N/A
AEROSPACI score: 0.14 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: GTP pyrophosphokinase YjbM
    Species: Bacillus subtilis PY79 [TaxId:1415167]
    Gene: yjbM, BSU11600
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5deda_
  • Chain 'B':
    Compound: GTP pyrophosphokinase YjbM
    Species: Bacillus subtilis PY79 [TaxId:1415167]
    Gene: yjbM, BSU11600
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5dedb_
  • Chain 'C':
    Compound: GTP pyrophosphokinase YjbM
    Species: Bacillus subtilis PY79 [TaxId:1415167]
    Gene: yjbM, BSU11600
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5dedc_
  • Chain 'D':
    Compound: GTP pyrophosphokinase YjbM
    Species: Bacillus subtilis PY79 [TaxId:1415167]
    Gene: yjbM, BSU11600
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5dedd_
  • Chain 'E':
    Compound: GTP pyrophosphokinase YjbM
    Species: Bacillus subtilis PY79 [TaxId:1415167]
    Gene: yjbM, BSU11600
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5dede_
  • Chain 'F':
    Compound: GTP pyrophosphokinase YjbM
    Species: Bacillus subtilis PY79 [TaxId:1415167]
    Gene: yjbM, BSU11600
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5dedf_
  • Chain 'G':
    Compound: GTP pyrophosphokinase YjbM
    Species: Bacillus subtilis PY79 [TaxId:1415167]
    Gene: yjbM, BSU11600
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5dedg_
  • Chain 'H':
    Compound: GTP pyrophosphokinase YjbM
    Species: Bacillus subtilis PY79 [TaxId:1415167]
    Gene: yjbM, BSU11600
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5dedh_
  • Heterogens: 0O2, MG

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5dedA (A:)
    mghhhhhhddkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasi
    lekarrksiplheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehke
    sgyrsyhlvvlyplqtvsgekhvlveiqirtlamnfwatiehslnykysgnipekvklrl
    qraseaasrldeemseirgevqeaqaafsrkkkgseqq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5dedA (A:)
    dkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasilekarrksi
    plheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehkesgyrsyhlv
    vlyplqtvsgekhvlveiqirtlamnfwatiehslnykysgnipekvklrlqraseaasr
    ldeemseirgevqeaa
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5dedB (B:)
    mghhhhhhddkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasi
    lekarrksiplheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehke
    sgyrsyhlvvlyplqtvsgekhvlveiqirtlamnfwatiehslnykysgnipekvklrl
    qraseaasrldeemseirgevqeaqaafsrkkkgseqq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5dedB (B:)
    dkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasilekarrksi
    plheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehkesgyrsyhlv
    vlyplqtvsgekhvlveiqirtlamnfwatiehslnyksgnekvklrlqraseaasrlde
    emseirgevaa
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5dedC (C:)
    mghhhhhhddkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasi
    lekarrksiplheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehke
    sgyrsyhlvvlyplqtvsgekhvlveiqirtlamnfwatiehslnykysgnipekvklrl
    qraseaasrldeemseirgevqeaqaafsrkkkgseqq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5dedC (C:)
    dkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasilekarrksi
    plheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehkesgyrsyhlv
    vlyplqtvsgekhvlveiqirtlamnfwatiehslnykysgnipekvklrlqraseaasr
    ldeemseirgevqe
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5dedD (D:)
    mghhhhhhddkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasi
    lekarrksiplheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehke
    sgyrsyhlvvlyplqtvsgekhvlveiqirtlamnfwatiehslnykysgnipekvklrl
    qraseaasrldeemseirgevqeaqaafsrkkkgseqq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5dedD (D:)
    dkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasilekarrksi
    plheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehkesgyrsyhlv
    vlyplqtvsgekhvlveiqirtlamnfwatiehslykpekvklrlqraseaasrldeems
    eirgvqea
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5dedE (E:)
    mghhhhhhddkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasi
    lekarrksiplheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehke
    sgyrsyhlvvlyplqtvsgekhvlveiqirtlamnfwatiehslnykysgnipekvklrl
    qraseaasrldeemseirgevqeaqaafsrkkkgseqq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5dedE (E:)
    dkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasilekarrksi
    plheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehkesgyrsyhlv
    vlyplqtvsgekhvlveiqirtlamnfwatiehslnykipekvklrlqraseaasrldee
    mseirgevqe
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >5dedF (F:)
    mghhhhhhddkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasi
    lekarrksiplheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehke
    sgyrsyhlvvlyplqtvsgekhvlveiqirtlamnfwatiehslnykysgnipekvklrl
    qraseaasrldeemseirgevqeaqaafsrkkkgseqq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5dedF (F:)
    dkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasilekarrksi
    plheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehkesgyrsyhlv
    vlyplqtvsgekhvlveiqirtlamnfwatiehslnyksgnipekvklrlqraseaasrl
    deemseirgeva
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >5dedG (G:)
    mghhhhhhddkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasi
    lekarrksiplheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehke
    sgyrsyhlvvlyplqtvsgekhvlveiqirtlamnfwatiehslnykysgnipekvklrl
    qraseaasrldeemseirgevqeaqaafsrkkkgseqq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5dedG (G:)
    dkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasilekarrksi
    plheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehkesgyrsyhlv
    vlyplqtvsgekhvlveiqirtlamnfwatiehslykipekvklrlqraseaasrldeem
    seirgevqea
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >5dedH (H:)
    mghhhhhhddkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasi
    lekarrksiplheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehke
    sgyrsyhlvvlyplqtvsgekhvlveiqirtlamnfwatiehslnykysgnipekvklrl
    qraseaasrldeemseirgevqeaqaafsrkkkgseqq
    

    Sequence, based on observed residues (ATOM records): (download)
    >5dedH (H:)
    dkqwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasilekarrksi
    plheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiaehkesgyrsyhlv
    vlyplqtvsgekhvlveiqirtlamnfwatiehslnykysgnipekvklrlqraseaasr
    ldeemseirgevaa