PDB entry 3ejx

View 3ejx on RCSB PDB site
Description: Crystal structure of diaminopimelate epimerase from Arabidopsis thaliana in complex with LL-AziDAP
Class: isomerase
Keywords: Diaminopimelate epimerase, Arabidopsis, PLP-independenet amino acid racemase, aziridino-diaminopimelate, crystal structure, ISOMERASE
Deposited on 2008-09-18, released 2009-02-17
The last revision prior to the SCOPe 2.08 freeze date was dated 2009-05-26, with a file datestamp of 2009-05-22.
Experiment type: XRAY
Resolution: 1.95 Å
R-factor: 0.179
AEROSPACI score: 0.46 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Diaminopimelate epimerase, chloroplastic
    Species: Arabidopsis thaliana [TaxId:3702]
    Gene: DAPF
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3ejxa1, d3ejxa2
  • Chain 'B':
    Compound: Diaminopimelate epimerase, chloroplastic
    Species: Arabidopsis thaliana [TaxId:3702]
    Gene: DAPF
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9LFG2 (Start-310)
      • expression tag (311)
    Domains in SCOPe 2.08: d3ejxb1, d3ejxb2, d3ejxb3
  • Chain 'C':
    Compound: Diaminopimelate epimerase, chloroplastic
    Species: Arabidopsis thaliana [TaxId:3702]
    Gene: DAPF
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3ejxc1, d3ejxc2
  • Chain 'D':
    Compound: Diaminopimelate epimerase, chloroplastic
    Species: Arabidopsis thaliana [TaxId:3702]
    Gene: DAPF
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3ejxd1, d3ejxd2
  • Chain 'E':
    Compound: Diaminopimelate epimerase, chloroplastic
    Species: Arabidopsis thaliana [TaxId:3702]
    Gene: DAPF
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3ejxe1, d3ejxe2
  • Chain 'F':
    Compound: Diaminopimelate epimerase, chloroplastic
    Species: Arabidopsis thaliana [TaxId:3702]
    Gene: DAPF
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3ejxf1, d3ejxf2
  • Heterogens: ZDP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >3ejxA (A:)
aaasmdavtaekfspasfldkketgvlhfvkyhglgndfilvdnrdssepkitqeqaakl
cdrnfgvgadgvifampgvngtdyamrifnsdgsepemcgngvrcfarfiaelenlqgkh
sftihtgaglivpeiqddgqvkvdmgtpilkaqdvptklsgnkgeavveaelvvdgvswn
vtcvsmgnphcitfgkkggpnlkvddlnlpeigpkfehhemfpartntefvevlsrshlk
mrvwergagatlacgtgacalvvaavlegradrkctvdlpggpleiewkqednhiymtgp
aeavfygsallhhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >3ejxA (A:)
gvlhfvkyhglgndfilvdnrdssepkitqeqaaklcdrnfgvgadgvifampgvngtdy
amrifnsdgsepemcgngvrcfarfiaelenlqgkhsftihtgaglivpeiqddgqvkvd
mgtpilkaqdvptklsgnkgeavveaelvvdgvswnvtcvsmgnphcitfgkkggpnlkv
ddlnlpeigpkfehhemfpartntefvevlsrshlkmrvwergagatlacgtgacalvva
avlegradrkctvdlpggpleiewkqednhiymtgpaeavfygsall

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >3ejxB (B:)
aaasmdavtaekfspasfldkketgvlhfvkyhglgndfilvdnrdssepkitqeqaakl
cdrnfgvgadgvifampgvngtdyamrifnsdgsepemcgngvrcfarfiaelenlqgkh
sftihtgaglivpeiqddgqvkvdmgtpilkaqdvptklsgnkgeavveaelvvdgvswn
vtcvsmgnphcitfgkkggpnlkvddlnlpeigpkfehhemfpartntefvevlsrshlk
mrvwergagatlacgtgacalvvaavlegradrkctvdlpggpleiewkqednhiymtgp
aeavfygsallhhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >3ejxB (B:)
gvlhfvkyhglgndfilvdnrdssepkitqeqaaklcdrnfgvgadgvifampgvngtdy
amrifnsdgsepemcgngvrcfarfiaelenlqgkhsftihtgaglivpeiqddgqvkvd
mgtpilkaqdvptklsgnkgeavveaelvvdgvswnvtcvsmgnphcitfgkkggpnlkv
ddlnlpeigpkfehhemfpartntefvevlsrshlkmrvwergagatlacgtgacalvva
avlegradrkctvdlpggpleiewkqednhiymtgpaeavfygsallh

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >3ejxC (C:)
aaasmdavtaekfspasfldkketgvlhfvkyhglgndfilvdnrdssepkitqeqaakl
cdrnfgvgadgvifampgvngtdyamrifnsdgsepemcgngvrcfarfiaelenlqgkh
sftihtgaglivpeiqddgqvkvdmgtpilkaqdvptklsgnkgeavveaelvvdgvswn
vtcvsmgnphcitfgkkggpnlkvddlnlpeigpkfehhemfpartntefvevlsrshlk
mrvwergagatlacgtgacalvvaavlegradrkctvdlpggpleiewkqednhiymtgp
aeavfygsallhhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >3ejxC (C:)
gvlhfvkyhglgndfilvdnrdssepkitqeqaaklcdrnfgvgadgvifampgvngtdy
amrifnsdgsepemcgngvrcfarfiaelenlqgkhsftihtgaglivpeiqddgqvkvd
mgtpilkaqdvptklsgnkgeavveaelvvdgvswnvtcvsmgnphcitfgkkggpnlkv
ddlnlpeigpkfehhemfpartntefvevlsrshlkmrvwergagatlacgtgacalvva
avlegradrkctvdlpggpleiewkqednhiymtgpaeavfygsall

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3ejxD (D:)
aaasmdavtaekfspasfldkketgvlhfvkyhglgndfilvdnrdssepkitqeqaakl
cdrnfgvgadgvifampgvngtdyamrifnsdgsepemcgngvrcfarfiaelenlqgkh
sftihtgaglivpeiqddgqvkvdmgtpilkaqdvptklsgnkgeavveaelvvdgvswn
vtcvsmgnphcitfgkkggpnlkvddlnlpeigpkfehhemfpartntefvevlsrshlk
mrvwergagatlacgtgacalvvaavlegradrkctvdlpggpleiewkqednhiymtgp
aeavfygsallhhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >3ejxD (D:)
ekfspasfldkketgvlhfvkyhglgndfilvdnrdssepkitqeqaaklcdrnfgvgad
gvifampgvngtdyamrifnsdgsepemcgngvrcfarfiaelenlqgkhsftihtgagl
ivpeiqddgqvkvdmgtpilkaqdvptklsgnkgeavveaelvvdgvswnvtcvsmgnph
citfgkkggpnlkvddlnlpeigpkfehhemfpartntefvevlsrshlkmrvwergaga
tlacgtgacalvvaavlegradrkctvdlpggpleiewkqednhiymtgpaeavfygsal
l

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >3ejxE (E:)
aaasmdavtaekfspasfldkketgvlhfvkyhglgndfilvdnrdssepkitqeqaakl
cdrnfgvgadgvifampgvngtdyamrifnsdgsepemcgngvrcfarfiaelenlqgkh
sftihtgaglivpeiqddgqvkvdmgtpilkaqdvptklsgnkgeavveaelvvdgvswn
vtcvsmgnphcitfgkkggpnlkvddlnlpeigpkfehhemfpartntefvevlsrshlk
mrvwergagatlacgtgacalvvaavlegradrkctvdlpggpleiewkqednhiymtgp
aeavfygsallhhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >3ejxE (E:)
gvlhfvkyhglgndfilvdnrdssepkitqeqaaklcdrnfgvgadgvifampgvngtdy
amrifnsdgsepemcgngvrcfarfiaelenlqgkhsftihtgaglivpeiqddgqvkvd
mgtpilkaqdvptklsgnkgeavveaelvvdgvswnvtcvsmgnphcitfgkkggpnlkv
ddlnlpeigpkfehhemfpartntefvevlsrshlkmrvwergagatlacgtgacalvva
avlegradrkctvdlpggpleiewkqednhiymtgpaeavfygsall

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >3ejxF (F:)
aaasmdavtaekfspasfldkketgvlhfvkyhglgndfilvdnrdssepkitqeqaakl
cdrnfgvgadgvifampgvngtdyamrifnsdgsepemcgngvrcfarfiaelenlqgkh
sftihtgaglivpeiqddgqvkvdmgtpilkaqdvptklsgnkgeavveaelvvdgvswn
vtcvsmgnphcitfgkkggpnlkvddlnlpeigpkfehhemfpartntefvevlsrshlk
mrvwergagatlacgtgacalvvaavlegradrkctvdlpggpleiewkqednhiymtgp
aeavfygsallhhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >3ejxF (F:)
ekfspasfldkketgvlhfvkyhglgndfilvdnrdssepkitqeqaaklcdrnfgvgad
gvifampgvngtdyamrifnsdgsepemcgngvrcfarfiaelenlqgkhsftihtgagl
ivpeiqddgqvkvdmgtpilkaqdvptklsgnkgeavveaelvvdgvswnvtcvsmgnph
citfgkkggpnlkvddlnlpeigpkfehhemfpartntefvevlsrshlkmrvwergaga
tlacgtgacalvvaavlegradrkctvdlpggpleiewkqednhiymtgpaeavfygsal
l