PDB entry 4fir

View 4fir on RCSB PDB site
Description: Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus
Class: lyase
Keywords: Pyrococcus horikoshii, pdxS, pyridoxal biosynthesis lyase, pyridoxal 5 -phosphate (PLP), lyase
Deposited on 2012-06-11, released 2012-11-14
The last revision prior to the SCOPe 2.08 freeze date was dated 2012-11-14, with a file datestamp of 2012-11-09.
Experiment type: XRAY
Resolution: 3.1 Å
R-factor: 0.187
AEROSPACI score: 0.25 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Pyridoxal biosynthesis lyase pdxS
    Species: Pyrococcus horikoshii [TaxId:70601]
    Gene: pdxS, PH1355
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4fira_
  • Chain 'B':
    Compound: Pyridoxal biosynthesis lyase pdxS
    Species: Pyrococcus horikoshii [TaxId:70601]
    Gene: pdxS, PH1355
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4firb_
  • Chain 'C':
    Compound: Pyridoxal biosynthesis lyase pdxS
    Species: Pyrococcus horikoshii [TaxId:70601]
    Gene: pdxS, PH1355
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4firc_
  • Chain 'D':
    Compound: Pyridoxal biosynthesis lyase pdxS
    Species: Pyrococcus horikoshii [TaxId:70601]
    Gene: pdxS, PH1355
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4fird_
  • Chain 'E':
    Compound: Pyridoxal biosynthesis lyase pdxS
    Species: Pyrococcus horikoshii [TaxId:70601]
    Gene: pdxS, PH1355
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4fire_
  • Chain 'F':
    Compound: Pyridoxal biosynthesis lyase pdxS
    Species: Pyrococcus horikoshii [TaxId:70601]
    Gene: pdxS, PH1355
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4firf_
  • Heterogens: R5P, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >4firA (A:)
mdklkiimekgterlkrgfakmvkggvimdvtnaeqariaeeagavavmalhkvpadirk
aggvarmapvekiqeimdavtipvmakcrigheaearilealgvdmidesevltpadpff
hiykkkftapfvcgarnlgeavrriwegaamirtkgeagtgniieavrhvrlvnenirli
qrmtdeeiygvaekfaepylrlafsvkeisglpkrvlenepiyegftyreivediykill
eikklgrlpvvnfaaggvatpadaalmmamgmdgvfvgsgifkssnppkmaraiveavnh
wdepdvlaeisreigepmrgqaieelqvrmeergi

    Sequence, based on observed residues (ATOM records): (download) 
    >4firA (A:)
mdklkiimekgterlkrgfakmvkggvimdvtnaeqariaeeagavavmalhkvpadirk
aggvarmapvekiqeimdavtipvmakcrigheaearilealgvdmidesevltpadpff
hiykkkftapfvcgarnlgeavrriwegaamirtkgeagtgniieavrhvrlvnenirli
qrmtdeeiygvaekfaepylrlafsvkeisglpkrvlenepiyegftyreivediykill
eikklgrlpvvnfaaggvatpadaalmmamgmdgvfvgsgifkssnppkmaraiveavnh
wdepdvlaeisreigepmrgqaieelqvrmeer

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >4firB (B:)
mdklkiimekgterlkrgfakmvkggvimdvtnaeqariaeeagavavmalhkvpadirk
aggvarmapvekiqeimdavtipvmakcrigheaearilealgvdmidesevltpadpff
hiykkkftapfvcgarnlgeavrriwegaamirtkgeagtgniieavrhvrlvnenirli
qrmtdeeiygvaekfaepylrlafsvkeisglpkrvlenepiyegftyreivediykill
eikklgrlpvvnfaaggvatpadaalmmamgmdgvfvgsgifkssnppkmaraiveavnh
wdepdvlaeisreigepmrgqaieelqvrmeergi

    Sequence, based on observed residues (ATOM records): (download) 
    >4firB (B:)
mdklkiimekgterlkrgfakmvkggvimdvtnaeqariaeeagavavmalhkvpadirk
aggvarmapvekiqeimdavtipvmakcrigheaearilealgvdmidesevltpadpff
hiykkkftapfvcgarnlgeavrriwegaamirtkgeagtgniieavrhvrlvnenirli
qrmtdeeiygvaekfaepylrlafsvkeisglpkrvlenepiyegftyreivediykill
eikklgrlpvvnfaaggvatpadaalmmamgmdgvfvgsgifkssnppkmaraiveavnh
wdepdvlaeisreigepmrgqaieelqvrmeer

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >4firC (C:)
mdklkiimekgterlkrgfakmvkggvimdvtnaeqariaeeagavavmalhkvpadirk
aggvarmapvekiqeimdavtipvmakcrigheaearilealgvdmidesevltpadpff
hiykkkftapfvcgarnlgeavrriwegaamirtkgeagtgniieavrhvrlvnenirli
qrmtdeeiygvaekfaepylrlafsvkeisglpkrvlenepiyegftyreivediykill
eikklgrlpvvnfaaggvatpadaalmmamgmdgvfvgsgifkssnppkmaraiveavnh
wdepdvlaeisreigepmrgqaieelqvrmeergi

    Sequence, based on observed residues (ATOM records): (download) 
    >4firC (C:)
mdklkiimekgterlkrgfakmvkggvimdvtnaeqariaeeagavavmalhkvpadirk
aggvarmapvekiqeimdavtipvmakcrigheaearilealgvdmidesevltpadpff
hiykkkftapfvcgarnlgeavrriwegaamirtkgeagtgniieavrhvrlvnenirli
qrmtdeeiygvaekfaepylrlafsvkeisglpkrvlenepiyegftyreivediykill
eikklgrlpvvnfaaggvatpadaalmmamgmdgvfvgsgifkssnppkmaraiveavnh
wdepdvlaeisreigepmrgqaieelqvrmeer

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >4firD (D:)
mdklkiimekgterlkrgfakmvkggvimdvtnaeqariaeeagavavmalhkvpadirk
aggvarmapvekiqeimdavtipvmakcrigheaearilealgvdmidesevltpadpff
hiykkkftapfvcgarnlgeavrriwegaamirtkgeagtgniieavrhvrlvnenirli
qrmtdeeiygvaekfaepylrlafsvkeisglpkrvlenepiyegftyreivediykill
eikklgrlpvvnfaaggvatpadaalmmamgmdgvfvgsgifkssnppkmaraiveavnh
wdepdvlaeisreigepmrgqaieelqvrmeergi

    Sequence, based on observed residues (ATOM records): (download) 
    >4firD (D:)
mdklkiimekgterlkrgfakmvkggvimdvtnaeqariaeeagavavmalhkvpadirk
aggvarmapvekiqeimdavtipvmakcrigheaearilealgvdmidesevltpadpff
hiykkkftapfvcgarnlgeavrriwegaamirtkgeagtgniieavrhvrlvnenirli
qrmtdeeiygvaekfaepylrlafsvkeisglpkrvlenepiyegftyreivediykill
eikklgrlpvvnfaaggvatpadaalmmamgmdgvfvgsgifkssnppkmaraiveavnh
wdepdvlaeisreigepmrgqaieelqvrmeer

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >4firE (E:)
mdklkiimekgterlkrgfakmvkggvimdvtnaeqariaeeagavavmalhkvpadirk
aggvarmapvekiqeimdavtipvmakcrigheaearilealgvdmidesevltpadpff
hiykkkftapfvcgarnlgeavrriwegaamirtkgeagtgniieavrhvrlvnenirli
qrmtdeeiygvaekfaepylrlafsvkeisglpkrvlenepiyegftyreivediykill
eikklgrlpvvnfaaggvatpadaalmmamgmdgvfvgsgifkssnppkmaraiveavnh
wdepdvlaeisreigepmrgqaieelqvrmeergi

    Sequence, based on observed residues (ATOM records): (download) 
    >4firE (E:)
mdklkiimekgterlkrgfakmvkggvimdvtnaeqariaeeagavavmalhkvpadirk
aggvarmapvekiqeimdavtipvmakcrigheaearilealgvdmidesevltpadpff
hiykkkftapfvcgarnlgeavrriwegaamirtkgeagtgniieavrhvrlvnenirli
qrmtdeeiygvaekfaepylrlafsvkeisglpkrvlenepiyegftyreivediykill
eikklgrlpvvnfaaggvatpadaalmmamgmdgvfvgsgifkssnppkmaraiveavnh
wdepdvlaeisreigepmrgqaieelqvrmeer

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >4firF (F:)
mdklkiimekgterlkrgfakmvkggvimdvtnaeqariaeeagavavmalhkvpadirk
aggvarmapvekiqeimdavtipvmakcrigheaearilealgvdmidesevltpadpff
hiykkkftapfvcgarnlgeavrriwegaamirtkgeagtgniieavrhvrlvnenirli
qrmtdeeiygvaekfaepylrlafsvkeisglpkrvlenepiyegftyreivediykill
eikklgrlpvvnfaaggvatpadaalmmamgmdgvfvgsgifkssnppkmaraiveavnh
wdepdvlaeisreigepmrgqaieelqvrmeergi

    Sequence, based on observed residues (ATOM records): (download) 
    >4firF (F:)
mdklkiimekgterlkrgfakmvkggvimdvtnaeqariaeeagavavmalhkvpadirk
aggvarmapvekiqeimdavtipvmakcrigheaearilealgvdmidesevltpadpff
hiykkkftapfvcgarnlgeavrriwegaamirtkgeagtgniieavrhvrlvnenirli
qrmtdeeiygvaekfaepylrlafsvkeisglpkrvlenepiyegftyreivediykill
eikklgrlpvvnfaaggvatpadaalmmamgmdgvfvgsgifkssnppkmaraiveavnh
wdepdvlaeisreigepmrgqaieelqvrmeer