PDB entry 3pef

View 3pef on RCSB PDB site
Description: Crystal structure of gamma-hydroxybutyrate dehydrogenase from Geobacter metallireducens in complex with NADP+
Class: oxidoreductase
Keywords: gamma-hydroxybutyrate dehydrogenase, succinic semialdehyde reductase, Geobacter metallireducens, NADP+, OXIDOREDUCTASE
Deposited on 2010-10-26, released 2011-12-07
The last revision prior to the SCOPe 2.07 freeze date was dated 2016-06-01, with a file datestamp of 2016-05-27.
Experiment type: XRAY
Resolution: 2.07 Å
R-factor: N/A
AEROSPACI score: 0.29 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 6-phosphogluconate dehydrogenase, NAD-binding
    Species: Geobacter metallireducens [TaxId:28232]
    Gene: Gmet_3011
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q39R98 (0-286)
      • engineered mutation (0)
      • engineered mutation (284)
    Domains in SCOPe 2.07: d3pefa1, d3pefa2
  • Chain 'B':
    Compound: 6-phosphogluconate dehydrogenase, NAD-binding
    Species: Geobacter metallireducens [TaxId:28232]
    Gene: Gmet_3011
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q39R98 (0-286)
      • engineered mutation (0)
      • engineered mutation (284)
    Domains in SCOPe 2.07: d3pefb1, d3pefb2
  • Chain 'C':
    Compound: 6-phosphogluconate dehydrogenase, NAD-binding
    Species: Geobacter metallireducens [TaxId:28232]
    Gene: Gmet_3011
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q39R98 (0-286)
      • engineered mutation (0)
      • engineered mutation (284)
    Domains in SCOPe 2.07: d3pefc1, d3pefc2
  • Chain 'D':
    Compound: 6-phosphogluconate dehydrogenase, NAD-binding
    Species: Geobacter metallireducens [TaxId:28232]
    Gene: Gmet_3011
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q39R98 (0-End)
      • engineered mutation (0)
      • engineered mutation (284)
    Domains in SCOPe 2.07: d3pefd1, d3pefd2
  • Chain 'E':
    Compound: 6-phosphogluconate dehydrogenase, NAD-binding
    Species: Geobacter metallireducens [TaxId:28232]
    Gene: Gmet_3011
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q39R98 (0-End)
      • engineered mutation (0)
      • engineered mutation (284)
    Domains in SCOPe 2.07: d3pefe1, d3pefe2
  • Chain 'F':
    Compound: 6-phosphogluconate dehydrogenase, NAD-binding
    Species: Geobacter metallireducens [TaxId:28232]
    Gene: Gmet_3011
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q39R98
      • engineered mutation (284)
    Domains in SCOPe 2.07: d3peff1, d3peff2
  • Chain 'G':
    Compound: 6-phosphogluconate dehydrogenase, NAD-binding
    Species: Geobacter metallireducens [TaxId:28232]
    Gene: Gmet_3011
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q39R98 (0-286)
      • engineered mutation (0)
      • engineered mutation (284)
    Domains in SCOPe 2.07: d3pefg1, d3pefg2
  • Chain 'H':
    Compound: 6-phosphogluconate dehydrogenase, NAD-binding
    Species: Geobacter metallireducens [TaxId:28232]
    Gene: Gmet_3011
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q39R98 (Start-286)
      • engineered mutation (284)
    Domains in SCOPe 2.07: d3pefh1, d3pefh2
  • Heterogens: NAP, GOL, PEG, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3pefA (A:)
    sqkfgfiglgimgsamaknlvkagcsvtiwnrspekaeelaalgaeraatpcevvescpv
    tfamladpaaaeevcfgkhgvlegigegrgyvdmstvdpatsqrigvavvakggrfleap
    vsgskkpaedgtliilaagdrnlydeampgfekmgkkiihlgdvgkgaemklvvnmvmgg
    mmacfceglalgekaglatdaildvigagamanpmfalkgglirdrnfapafplkhmqkd
    lrlavalgdrvgqplvasaaanelfkgaraagfgdedfsaifktyer
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3pefB (B:)
    sqkfgfiglgimgsamaknlvkagcsvtiwnrspekaeelaalgaeraatpcevvescpv
    tfamladpaaaeevcfgkhgvlegigegrgyvdmstvdpatsqrigvavvakggrfleap
    vsgskkpaedgtliilaagdrnlydeampgfekmgkkiihlgdvgkgaemklvvnmvmgg
    mmacfceglalgekaglatdaildvigagamanpmfalkgglirdrnfapafplkhmqkd
    lrlavalgdrvgqplvasaaanelfkgaraagfgdedfsaifktyer
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3pefC (C:)
    sqkfgfiglgimgsamaknlvkagcsvtiwnrspekaeelaalgaeraatpcevvescpv
    tfamladpaaaeevcfgkhgvlegigegrgyvdmstvdpatsqrigvavvakggrfleap
    vsgskkpaedgtliilaagdrnlydeampgfekmgkkiihlgdvgkgaemklvvnmvmgg
    mmacfceglalgekaglatdaildvigagamanpmfalkgglirdrnfapafplkhmqkd
    lrlavalgdrvgqplvasaaanelfkgaraagfgdedfsaifktyer
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3pefD (D:)
    sqkfgfiglgimgsamaknlvkagcsvtiwnrspekaeelaalgaeraatpcevvescpv
    tfamladpaaaeevcfgkhgvlegigegrgyvdmstvdpatsqrigvavvakggrfleap
    vsgskkpaedgtliilaagdrnlydeampgfekmgkkiihlgdvgkgaemklvvnmvmgg
    mmacfceglalgekaglatdaildvigagamanpmfalkgglirdrnfapafplkhmqkd
    lrlavalgdrvgqplvasaaanelfkgaraagfgdedfsaifktyer
    

    Sequence, based on observed residues (ATOM records): (download)
    >3pefD (D:)
    sqkfgfiglgimgsamaknlvkagcsvtiwnrspekaeelaalgaeraatpcevvescpv
    tfamladpaaaeevcfgkhgvlegigegrgyvdmstvdpatsqrigvavvakggrfleap
    vsgskkpaedgtliilaagdrnlydeampgfekmgkkiihlgdvgkgaemklvvnmvmgg
    mmacfceglalgekaglatdaildvigagamanpmfalkgglirdrnfapafplkhmqkd
    lrlavalgdrvgqplvasaaanelfkgaraagfgdedfsaifktye
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3pefE (E:)
    sqkfgfiglgimgsamaknlvkagcsvtiwnrspekaeelaalgaeraatpcevvescpv
    tfamladpaaaeevcfgkhgvlegigegrgyvdmstvdpatsqrigvavvakggrfleap
    vsgskkpaedgtliilaagdrnlydeampgfekmgkkiihlgdvgkgaemklvvnmvmgg
    mmacfceglalgekaglatdaildvigagamanpmfalkgglirdrnfapafplkhmqkd
    lrlavalgdrvgqplvasaaanelfkgaraagfgdedfsaifktyer
    

    Sequence, based on observed residues (ATOM records): (download)
    >3pefE (E:)
    sqkfgfiglgimgsamaknlvkagcsvtiwnrspekaeelaalgaeraatpcevvescpv
    tfamladpaaaeevcfgkhgvlegigegrgyvdmstvdpatsqrigvavvakggrfleap
    vsgskkpaedgtliilaagdrnlydeampgfekmgkkiihlgdvgkgaemklvvnmvmgg
    mmacfceglalgekaglatdaildvigagamanpmfalkgglirdrnfapafplkhmqkd
    lrlavalgdrvgqplvasaaanelfkgaraagfgdedfsaifktye
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3pefF (F:)
    sqkfgfiglgimgsamaknlvkagcsvtiwnrspekaeelaalgaeraatpcevvescpv
    tfamladpaaaeevcfgkhgvlegigegrgyvdmstvdpatsqrigvavvakggrfleap
    vsgskkpaedgtliilaagdrnlydeampgfekmgkkiihlgdvgkgaemklvvnmvmgg
    mmacfceglalgekaglatdaildvigagamanpmfalkgglirdrnfapafplkhmqkd
    lrlavalgdrvgqplvasaaanelfkgaraagfgdedfsaifktyer
    

    Sequence, based on observed residues (ATOM records): (download)
    >3pefF (F:)
    qkfgfiglgimgsamaknlvkagcsvtiwnrspekaeelaalgaeraatpcevvescpvt
    famladpaaaeevcfgkhgvlegigegrgyvdmstvdpatsqrigvavvakggrfleapv
    sgskkpaedgtliilaagdrnlydeampgfekmgkkiihlgdvgkgaemklvvnmvmggm
    macfceglalgekaglatdaildvigagamanpmfalkgglirdrnfapafplkhmqkdl
    rlavalgdrvgqplvasaaanelfkgaraagfgdedfsaifktye
    

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3pefG (G:)
    sqkfgfiglgimgsamaknlvkagcsvtiwnrspekaeelaalgaeraatpcevvescpv
    tfamladpaaaeevcfgkhgvlegigegrgyvdmstvdpatsqrigvavvakggrfleap
    vsgskkpaedgtliilaagdrnlydeampgfekmgkkiihlgdvgkgaemklvvnmvmgg
    mmacfceglalgekaglatdaildvigagamanpmfalkgglirdrnfapafplkhmqkd
    lrlavalgdrvgqplvasaaanelfkgaraagfgdedfsaifktyer
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >3pefH (H:)
    sqkfgfiglgimgsamaknlvkagcsvtiwnrspekaeelaalgaeraatpcevvescpv
    tfamladpaaaeevcfgkhgvlegigegrgyvdmstvdpatsqrigvavvakggrfleap
    vsgskkpaedgtliilaagdrnlydeampgfekmgkkiihlgdvgkgaemklvvnmvmgg
    mmacfceglalgekaglatdaildvigagamanpmfalkgglirdrnfapafplkhmqkd
    lrlavalgdrvgqplvasaaanelfkgaraagfgdedfsaifktyer
    

    Sequence, based on observed residues (ATOM records): (download)
    >3pefH (H:)
    qkfgfiglgimgsamaknlvkagcsvtiwnrspekaeelaalgaeraatpcevvescpvt
    famladpaaaeevcfgkhgvlegigegrgyvdmstvdpatsqrigvavvakggrfleapv
    sgskkpaedgtliilaagdrnlydeampgfekmgkkiihlgdvgkgaemklvvnmvmggm
    macfceglalgekaglatdaildvigagamanpmfalkgglirdrnfapafplkhmqkdl
    rlavalgdrvgqplvasaaanelfkgaraagfgdedfsaifktyer