PDB entry 2nx3

View 2nx3 on RCSB PDB site
Description: Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase
Class: transferase
Keywords: kdo, kdo8p, kdo8ps, pep, a5p, transferase
Deposited on 2006-11-16, released 2007-04-24
The last revision prior to the SCOPe 2.07 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 2.1 Å
R-factor: 0.216
AEROSPACI score: 0.39 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Aquifex aeolicus [TaxId:63363]
    Gene: kdsA
    Database cross-references and differences (RAF-indexed):
    • Uniprot O66496
      • engineered (10)
      • engineered (234)
      • engineered (236)
    Domains in SCOPe 2.07: d2nx3a_
  • Chain 'B':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Aquifex aeolicus [TaxId:63363]
    Gene: kdsA
    Database cross-references and differences (RAF-indexed):
    • Uniprot O66496
      • engineered (10)
      • engineered (234)
      • engineered (236)
    Domains in SCOPe 2.07: d2nx3b_
  • Chain 'C':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Aquifex aeolicus [TaxId:63363]
    Gene: kdsA
    Database cross-references and differences (RAF-indexed):
    • Uniprot O66496
      • engineered (10)
      • engineered (234)
      • engineered (236)
    Domains in SCOPe 2.07: d2nx3c_
  • Chain 'D':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Aquifex aeolicus [TaxId:63363]
    Gene: kdsA
    Database cross-references and differences (RAF-indexed):
    • Uniprot O66496
      • engineered (10)
      • engineered (234)
      • engineered (236)
    Domains in SCOPe 2.07: d2nx3d_
  • Chain 'E':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Aquifex aeolicus [TaxId:63363]
    Gene: kdsA
    Database cross-references and differences (RAF-indexed):
    • Uniprot O66496
      • engineered (10)
      • engineered (234)
      • engineered (236)
    Domains in SCOPe 2.07: d2nx3e_
  • Chain 'F':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Aquifex aeolicus [TaxId:63363]
    Gene: kdsA
    Database cross-references and differences (RAF-indexed):
    • Uniprot O66496
      • engineered (10)
      • engineered (234)
      • engineered (236)
    Domains in SCOPe 2.07: d2nx3f_
  • Chain 'G':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Aquifex aeolicus [TaxId:63363]
    Gene: kdsA
    Database cross-references and differences (RAF-indexed):
    • Uniprot O66496
      • engineered (10)
      • engineered (234)
      • engineered (236)
    Domains in SCOPe 2.07: d2nx3g_
  • Chain 'H':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Aquifex aeolicus [TaxId:63363]
    Gene: kdsA
    Database cross-references and differences (RAF-indexed):
    • Uniprot O66496
      • engineered (10)
      • engineered (234)
      • engineered (236)
    Domains in SCOPe 2.07: d2nx3h_
  • Chain 'I':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Aquifex aeolicus [TaxId:63363]
    Gene: kdsA
    Database cross-references and differences (RAF-indexed):
    • Uniprot O66496
      • engineered (10)
      • engineered (234)
      • engineered (236)
    Domains in SCOPe 2.07: d2nx3i_
  • Chain 'J':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Aquifex aeolicus [TaxId:63363]
    Gene: kdsA
    Database cross-references and differences (RAF-indexed):
    • Uniprot O66496
      • engineered (10)
      • engineered (234)
      • engineered (236)
    Domains in SCOPe 2.07: d2nx3j_
  • Chain 'K':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Aquifex aeolicus [TaxId:63363]
    Gene: kdsA
    Database cross-references and differences (RAF-indexed):
    • Uniprot O66496
      • engineered (10)
      • engineered (234)
      • engineered (236)
    Domains in SCOPe 2.07: d2nx3k_
  • Chain 'L':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Aquifex aeolicus [TaxId:63363]
    Gene: kdsA
    Database cross-references and differences (RAF-indexed):
    • Uniprot O66496
      • engineered (10)
      • engineered (234)
      • engineered (236)
    Domains in SCOPe 2.07: d2nx3l_
  • Heterogens: PEP, A5P, 1NT, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >2nx3A (A:)
mekflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgl
eygvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgra
vnvkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakvi
ydathsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalpl
sqlegiieaileirevaskyyetipvk

    Sequence, based on observed residues (ATOM records): (download) 
    >2nx3A (A:)
kflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgley
gvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgravn
vkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakviyd
athsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalplsq
legiieaileirevaskyyeti

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >2nx3B (B:)
mekflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgl
eygvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgra
vnvkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakvi
ydathsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalpl
sqlegiieaileirevaskyyetipvk

    Sequence, based on observed residues (ATOM records): (download) 
    >2nx3B (B:)
kflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgley
gvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgravn
vkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakviyd
athsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalplsq
legiieaileirevaskyyeti

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >2nx3C (C:)
mekflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgl
eygvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgra
vnvkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakvi
ydathsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalpl
sqlegiieaileirevaskyyetipvk

    Sequence, based on observed residues (ATOM records): (download) 
    >2nx3C (C:)
kflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgley
gvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgravn
vkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakviyd
athsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalplsq
legiieaileirevaskyyeti

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >2nx3D (D:)
mekflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgl
eygvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgra
vnvkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakvi
ydathsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalpl
sqlegiieaileirevaskyyetipvk

    Sequence, based on observed residues (ATOM records): (download) 
    >2nx3D (D:)
kflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgley
gvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgravn
vkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakviyd
athsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalplsq
legiieaileirevaskyyeti

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >2nx3E (E:)
mekflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgl
eygvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgra
vnvkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakvi
ydathsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalpl
sqlegiieaileirevaskyyetipvk

    Sequence, based on observed residues (ATOM records): (download) 
    >2nx3E (E:)
kflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgley
gvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgravn
vkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakviyd
athsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalplsq
legiieaileirevaskyyeti

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >2nx3F (F:)
mekflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgl
eygvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgra
vnvkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakvi
ydathsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalpl
sqlegiieaileirevaskyyetipvk

    Sequence, based on observed residues (ATOM records): (download) 
    >2nx3F (F:)
kflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgley
gvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgravn
vkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakviyd
athsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalplsq
legiieaileirevaskyyeti

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >2nx3G (G:)
mekflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgl
eygvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgra
vnvkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakvi
ydathsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalpl
sqlegiieaileirevaskyyetipvk

    Sequence, based on observed residues (ATOM records): (download) 
    >2nx3G (G:)
kflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgley
gvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgravn
vkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakviyd
athsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalplsq
legiieaileirevaskyyeti

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >2nx3H (H:)
mekflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgl
eygvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgra
vnvkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakvi
ydathsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalpl
sqlegiieaileirevaskyyetipvk

    Sequence, based on observed residues (ATOM records): (download) 
    >2nx3H (H:)
kflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgley
gvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgravn
vkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakviyd
athsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalplsq
legiieaileirevaskyyeti

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >2nx3I (I:)
mekflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgl
eygvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgra
vnvkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakvi
ydathsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalpl
sqlegiieaileirevaskyyetipvk

    Sequence, based on observed residues (ATOM records): (download) 
    >2nx3I (I:)
kflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgley
gvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgravn
vkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakviyd
athsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalplsq
legiieaileirevaskyyeti

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >2nx3J (J:)
mekflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgl
eygvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgra
vnvkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakvi
ydathsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalpl
sqlegiieaileirevaskyyetipvk

    Sequence, based on observed residues (ATOM records): (download) 
    >2nx3J (J:)
kflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgley
gvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgravn
vkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakviyd
athsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalplsq
legiieaileirevaskyyeti

  • Chain 'K':
    Sequence, based on SEQRES records: (download) 
    >2nx3K (K:)
mekflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgl
eygvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgra
vnvkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakvi
ydathsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalpl
sqlegiieaileirevaskyyetipvk

    Sequence, based on observed residues (ATOM records): (download) 
    >2nx3K (K:)
kflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgley
gvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgravn
vkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakviyd
athsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalplsq
legiieaileirevaskyyeti

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >2nx3L (L:)
mekflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgl
eygvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgra
vnvkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakvi
ydathsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalpl
sqlegiieaileirevaskyyetipvk

    Sequence, based on observed residues (ATOM records): (download) 
    >2nx3L (L:)
kflviagpnaieseelllkvgeeikrlsekfkevefvfkssfdkanrssihsfrghgley
gvkalrkvkeefglkittdiheswqaepvaevadiiqipaflcrqtdlllaaaktgravn
vkkgqflapwdtknvveklkfggakeiyltergttfgynnlvvdfrslpimkqwakviyd
athsvqlpgglgdksggmrefifpliraavavgcdgvfmethpepekalsdaptalplsq
legiieaileirevaskyyeti