PDB entry 5dec

View 5dec on RCSB PDB site
Description: Crystal structure of the small alarmone synthetase 1 from Bacillus subtilis
Class: transferase
Keywords: (p)ppGpp, stringent response, alarmone, allosteric regulator, transferase
Deposited on 2015-08-25, released 2015-10-28
The last revision prior to the SCOPe 2.05 freeze date was dated 2015-10-28, with a file datestamp of 2015-10-23.
Experiment type: XRAY
Resolution: 2 Å
R-factor: N/A
AEROSPACI score: 0.32 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: GTP pyrophosphokinase YjbM
    Species: Bacillus subtilis (strain 168) [TaxId:224308]
    Gene: yjbM, BSU11600
    Database cross-references and differences (RAF-indexed):
    • Uniprot O31611
      • conflict (10-11)
    Domains in SCOPe 2.05: d5deca_
  • Chain 'B':
    Compound: GTP pyrophosphokinase YjbM
    Species: Bacillus subtilis (strain 168) [TaxId:224308]
    Gene: yjbM, BSU11600
    Database cross-references and differences (RAF-indexed):
    • Uniprot O31611
      • conflict (10-11)
    Domains in SCOPe 2.05: d5decb_
  • Chain 'C':
    Compound: GTP pyrophosphokinase YjbM
    Species: Bacillus subtilis (strain 168) [TaxId:224308]
    Gene: yjbM, BSU11600
    Database cross-references and differences (RAF-indexed):
    • Uniprot O31611
      • conflict (10-11)
    Domains in SCOPe 2.05: d5decc_
  • Chain 'D':
    Compound: GTP pyrophosphokinase YjbM
    Species: Bacillus subtilis (strain 168) [TaxId:224308]
    Gene: yjbM, BSU11600
    Database cross-references and differences (RAF-indexed):
    • Uniprot O31611
      • conflict (10-11)
    Domains in SCOPe 2.05: d5decd_
  • Heterogens: HOH

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download)
    >5decA (A:)
    ddkwerflvpyrqaveelkvklkgirtlyeddhspiefvtgrvkpvasilekarrksipl
    heietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiagyrsyhlvvlyplqt
    vsgekhvlveiqirtlamnfwatiehslnykysgnipekvklrlqraseaasrldeemse
    irgevqea
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >5decB (B:)
    ddkwerflvpyrqaveelkvklkgirtlyedhspiefvtgrvkpvasilekarrksiplh
    eietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiahkesgyrsyhlvvlyp
    lqtvsgekhvlveiqirtlamnfwatiehslnykysgnipekvklrlqraseaasrldee
    mseirgevqea
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >5decC (C:)
    ddkwerflvpyrqaveelkvklkgirtlyeyeddhspiefvtgrvkpvasilekarrksi
    plheietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrsyhlvvlyplqtvsgek
    hvlveiqirtlamnfwatiehslnykysgnipekvklrlqraseaasrldeemseirgev
    qea
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >5decD (D:)
    ddkwerflvpyrqaveelkvklkgirtlyeddhspiefvtgrvkpvasilekarrksipl
    heietmqdiaglrimcqfvddiqivkemlfarkdftvvdqrdyiasgyrsyhlvvlyplq
    tvsgekhvlveiqirtlamnfwatiehslnykysgnipekvklrlqraseaasrldeems
    eirgevqea