PDB entry 2jer

View 2jer on RCSB PDB site
Description: agmatine deiminase of enterococcus faecalis catalyzing its reaction.
Class: hydrolase
Keywords: hydrolase, agmatine deiminase, tetramer, agdi, 5- fold pseudosymmetric structure, agmatine degradation pathway, covalent amidino adduct, agmatine iminohydrolase
Deposited on 2007-01-19, released 2007-01-30
The last revision prior to the SCOPe 2.07 freeze date was dated 2009-06-09, with a file datestamp of 2009-06-05.
Experiment type: XRAY
Resolution: 1.65 Å
R-factor: 0.168
AEROSPACI score: 0.58 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: agmatine deiminase
    Species: ENTEROCOCCUS FAECALIS [TaxId:1351]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q837U5 (Start-364)
      • conflict (324)
    • PDB 2JER (365-End)
    Domains in SCOPe 2.07: d2jera1
  • Chain 'B':
    Compound: agmatine deiminase
    Species: ENTEROCOCCUS FAECALIS [TaxId:1351]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q837U5 (Start-364)
      • conflict (324)
    • PDB 2JER
    Domains in SCOPe 2.07: d2jerb_
  • Chain 'C':
    Compound: agmatine deiminase
    Species: ENTEROCOCCUS FAECALIS [TaxId:1351]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q837U5 (Start-364)
      • conflict (324)
    • PDB 2JER (365-End)
    Domains in SCOPe 2.07: d2jerc_
  • Chain 'D':
    Compound: agmatine deiminase
    Species: ENTEROCOCCUS FAECALIS [TaxId:1351]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q837U5 (Start-364)
      • conflict (324)
    • PDB 2JER (365-End)
    Domains in SCOPe 2.07: d2jerd2, d2jerd3
  • Chain 'E':
    Compound: agmatine deiminase
    Species: ENTEROCOCCUS FAECALIS [TaxId:1351]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q837U5 (0-364)
      • conflict (324)
    • PDB 2JER (365-End)
    Domains in SCOPe 2.07: d2jere_
  • Chain 'F':
    Compound: agmatine deiminase
    Species: ENTEROCOCCUS FAECALIS [TaxId:1351]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q837U5 (Start-364)
      • conflict (324)
    • PDB 2JER (365-End)
    Domains in SCOPe 2.07: d2jerf_
  • Chain 'G':
    Compound: agmatine deiminase
    Species: ENTEROCOCCUS FAECALIS [TaxId:1351]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q837U5 (Start-364)
      • conflict (324)
    • PDB 2JER (365-End)
    Domains in SCOPe 2.07: d2jerg_
  • Chain 'H':
    Compound: agmatine deiminase
    Species: ENTEROCOCCUS FAECALIS [TaxId:1351]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q837U5 (Start-364)
      • conflict (324)
    • PDB 2JER (365-End)
    Domains in SCOPe 2.07: d2jerh_
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >2jerA (A:)
makrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqft
pmnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawg
glvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllseg
rnpqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqn
spfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdic
iasymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitq
qepkrvggkqnsssvdklaaalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >2jerA (A:)
akrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqftp
mnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawgg
lvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllsegr
npqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqns
pfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdici
asymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitqq
epkrvg

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >2jerB (B:)
makrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqft
pmnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawg
glvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllseg
rnpqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqn
spfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdic
iasymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitq
qepkrvggkqnsssvdklaaalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >2jerB (B:)
akrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqftp
mnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawgg
lvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllsegr
npqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqns
pfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdici
asymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitqq
epkr

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >2jerC (C:)
makrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqft
pmnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawg
glvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllseg
rnpqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqn
spfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdic
iasymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitq
qepkrvggkqnsssvdklaaalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >2jerC (C:)
akrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqftp
mnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawgg
lvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllsegr
npqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqns
pfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdici
asymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitqq
epkrvgg

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >2jerD (D:)
makrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqft
pmnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawg
glvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllseg
rnpqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqn
spfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdic
iasymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitq
qepkrvggkqnsssvdklaaalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >2jerD (D:)
akrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqftp
mnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawgg
lvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllsegr
npqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqns
pfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdici
asymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitqq
epkrvggkqnss

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >2jerE (E:)
makrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqft
pmnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawg
glvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllseg
rnpqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqn
spfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdic
iasymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitq
qepkrvggkqnsssvdklaaalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >2jerE (E:)
makrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqft
pmnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawg
glvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllseg
rnpqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqn
spfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdic
iasymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitq
qepkrvgg

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >2jerF (F:)
makrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqft
pmnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawg
glvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllseg
rnpqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqn
spfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdic
iasymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitq
qepkrvggkqnsssvdklaaalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >2jerF (F:)
akrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqftp
mnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawgg
lvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllsegr
npqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqns
pfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdici
asymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitqq
epkrvgg

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >2jerG (G:)
makrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqft
pmnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawg
glvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllseg
rnpqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqn
spfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdic
iasymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitq
qepkrvggkqnsssvdklaaalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >2jerG (G:)
akrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqftp
mnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawgg
lvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllsegr
npqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqns
pfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdici
asymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitqq
epkrvg

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >2jerH (H:)
makrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqft
pmnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawg
glvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllseg
rnpqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqn
spfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdic
iasymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitq
qepkrvggkqnsssvdklaaalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >2jerH (H:)
akrivgstpkqdgfrmpgefepqekvwmiwperpdnwrdggkpvqeaftnvakaisqftp
mnvvvsqqqfqncrrqlppeitvyemsnndawvrdcgpsfvindhgeirgvdwtfnawgg
lvdglyfpwdqddlvaqkiceiehvdsyrtddfvleggsfhvdgqgtvlttemcllsegr
npqlskeaieqklcdylnvekvlwlgdgidpeetnghvddvacfiapgevaciytedqns
pfyeaaqdayqrllkmtdakgrqlkvhklccpvknvtikgsfkidfvegtmpredgdici
asymnflitndgvivpqygdendrlaleqvqtmfpdkkivgvntvevvygggnihxitqq
epkrv