PDB entry 2nv1

View 2nv1 on RCSB PDB site
Description: Structure of the synthase subunit Pdx1 (YaaD) of PLP synthase from Bacillus subtilis
Class: lyase
Keywords: (beta/alpha)8-barrel, Synthase, LYASE
Deposited on 2006-11-10, released 2006-12-05
The last revision prior to the SCOPe 2.07 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-08.
Experiment type: XRAY
Resolution: 2.08 Å
R-factor: 0.144
AEROSPACI score: 0.49 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Pyridoxal biosynthesis lyase pdxS
    Species: Bacillus subtilis [TaxId:1423]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2nv1a_
  • Chain 'B':
    Compound: Pyridoxal biosynthesis lyase pdxS
    Species: Bacillus subtilis [TaxId:1423]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2nv1b_
  • Chain 'C':
    Compound: Pyridoxal biosynthesis lyase pdxS
    Species: Bacillus subtilis [TaxId:1423]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2nv1c_
  • Chain 'D':
    Compound: Pyridoxal biosynthesis lyase pdxS
    Species: Bacillus subtilis [TaxId:1423]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2nv1d_
  • Chain 'E':
    Compound: Pyridoxal biosynthesis lyase pdxS
    Species: Bacillus subtilis [TaxId:1423]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2nv1e_
  • Chain 'F':
    Compound: Pyridoxal biosynthesis lyase pdxS
    Species: Bacillus subtilis [TaxId:1423]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d2nv1f_
  • Heterogens: CL, MG, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2nv1A (A:)
    masmaqtgtervkrgmaemqkggvimdvinaeqakiaeeagavavmalervpadiraagg
    varmadptiveevmnavsipvmakarighivearvleamgvdyidesevltpadeefhln
    kneytvpfvcgcrdlgeatrriaegasmlrtkgepgtgniveavrhmrkvnaqvrkvvam
    sedelmteaknlgapyelllqikkdgklpvvnfaaggvatpadaalmmqlgadgvfvgsg
    ifksdnpakfakaiveatthftdykliaelskelgtamkgieisnllpeqrmqergwleh
    hhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nv1A (A:)
    tervkrgmaemqkggvimdvinaeqakiaeeagavavmaleraggvarmadptiveevmn
    avsipvmakarighivearvleamgvdyidesevltpadeefhlnkneytvpfvcgcrdl
    geatrriaegasmlrtkgepgtgniveavrhmrkvnaqvrkvvamsedelmteaknlgap
    yelllqikkdgklpvvnfaaggvatpadaalmmqlgadgvfvgsgifksdnpakfakaiv
    eatthftdykliaelskel
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2nv1B (B:)
    masmaqtgtervkrgmaemqkggvimdvinaeqakiaeeagavavmalervpadiraagg
    varmadptiveevmnavsipvmakarighivearvleamgvdyidesevltpadeefhln
    kneytvpfvcgcrdlgeatrriaegasmlrtkgepgtgniveavrhmrkvnaqvrkvvam
    sedelmteaknlgapyelllqikkdgklpvvnfaaggvatpadaalmmqlgadgvfvgsg
    ifksdnpakfakaiveatthftdykliaelskelgtamkgieisnllpeqrmqergwleh
    hhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nv1B (B:)
    krgmaemqkggvimdvinaeqakiaeeagavavmalergvarmadptiveevmnavsipv
    makarighivearvleamgvdyidesevltpadeefhlnkneytvpfvcgcrdlgeatrr
    iaegasmlrtkgepgtgniveavrhmrkvnaqvrkvvamsedelmteaknlgapyelllq
    ikkdgklpvvnfaaggvatpadaalmmqlgadgvfvgsgifksdnpakfakaiveatthf
    tdykliaelske
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2nv1C (C:)
    masmaqtgtervkrgmaemqkggvimdvinaeqakiaeeagavavmalervpadiraagg
    varmadptiveevmnavsipvmakarighivearvleamgvdyidesevltpadeefhln
    kneytvpfvcgcrdlgeatrriaegasmlrtkgepgtgniveavrhmrkvnaqvrkvvam
    sedelmteaknlgapyelllqikkdgklpvvnfaaggvatpadaalmmqlgadgvfvgsg
    ifksdnpakfakaiveatthftdykliaelskelgtamkgieisnllpeqrmqergwleh
    hhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nv1C (C:)
    ervkrgmaemqkggvimdvinaeqakiaeeagavavmalergvarmadptiveevmnavs
    ipvmakarighivearvleamgvdyidesevltpadeefhlnkneytvpfvcgcrdlgea
    trriaegasmlrtkgepgtgniveavrhmrkvnaqvrkvvamsedelmteaknlgapyel
    llqikkdgklpvvnfaaggvatpadaalmmqlgadgvfvgsgifksdnpakfakaiveat
    thftdykliaelskel
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2nv1D (D:)
    masmaqtgtervkrgmaemqkggvimdvinaeqakiaeeagavavmalervpadiraagg
    varmadptiveevmnavsipvmakarighivearvleamgvdyidesevltpadeefhln
    kneytvpfvcgcrdlgeatrriaegasmlrtkgepgtgniveavrhmrkvnaqvrkvvam
    sedelmteaknlgapyelllqikkdgklpvvnfaaggvatpadaalmmqlgadgvfvgsg
    ifksdnpakfakaiveatthftdykliaelskelgtamkgieisnllpeqrmqergwleh
    hhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nv1D (D:)
    rvkrgmaemqkggvimdvinaeqakiaeeagavavmalergvarmadptiveevmnavsi
    pvmakarighivearvleamgvdyidesevltpadeefhlnkneytvpfvcgcrdlgeat
    rriaegasmlrtkgepgtgniveavrhmrkvnaqvrkvvamsedelmteaknlgapyell
    lqikkdgklpvvnfaaggvatpadaalmmqlgadgvfvgsgifksdnpakfakaiveatt
    hftdykliaelskelg
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2nv1E (E:)
    masmaqtgtervkrgmaemqkggvimdvinaeqakiaeeagavavmalervpadiraagg
    varmadptiveevmnavsipvmakarighivearvleamgvdyidesevltpadeefhln
    kneytvpfvcgcrdlgeatrriaegasmlrtkgepgtgniveavrhmrkvnaqvrkvvam
    sedelmteaknlgapyelllqikkdgklpvvnfaaggvatpadaalmmqlgadgvfvgsg
    ifksdnpakfakaiveatthftdykliaelskelgtamkgieisnllpeqrmqergwleh
    hhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nv1E (E:)
    tervkrgmaemqkggvimdvinaeqakiaeeagavavmalergvarmadptiveevmnav
    sipvmakarighivearvleamgvdyidesevltpadeefhlnkneytvpfvcgcrdlge
    atrriaegasmlrtkgepgtgniveavrhmrkvnaqvrkvvamsedelmteaknlgapye
    lllqikkdgklpvvnfaaggvatpadaalmmqlgadgvfvgsgifksdnpakfakaivea
    tthftdykliaelske
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >2nv1F (F:)
    masmaqtgtervkrgmaemqkggvimdvinaeqakiaeeagavavmalervpadiraagg
    varmadptiveevmnavsipvmakarighivearvleamgvdyidesevltpadeefhln
    kneytvpfvcgcrdlgeatrriaegasmlrtkgepgtgniveavrhmrkvnaqvrkvvam
    sedelmteaknlgapyelllqikkdgklpvvnfaaggvatpadaalmmqlgadgvfvgsg
    ifksdnpakfakaiveatthftdykliaelskelgtamkgieisnllpeqrmqergwleh
    hhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >2nv1F (F:)
    gmaemqkggvimdvinaeqakiaeeagavavmalegvarmadptiveevmnavsipvmak
    arighivearvleamgvdyidesevltpadeefhlnkneytvpfvcgcrdlgeatrriae
    gasmlrtkgepgtgniveavrhmrkvnaqvrkvvamsedelmteaknlgapyelllqikk
    dgklpvvnfaaggvatpadaalmmqlgadgvfvgsgifksdnpakfakaiveatthftdy
    kliaelskel