PDB entry 4ycw

View 4ycw on RCSB PDB site
Description: Crystal structure of cladosporin in complex with plasmodium like human lysyl-tRNA synthetase mutant
Class: ligase/ligase inhibitor
Keywords: Inhibitor, Complex, LysRS, cladosporin, ligase-ligase inhibitor complex
Deposited on 2015-02-20, released 2015-06-10
The last revision prior to the SCOPe 2.05 freeze date was dated 2015-06-10, with a file datestamp of 2015-06-05.
Experiment type: XRAY
Resolution: 2.9 Å
R-factor: N/A
AEROSPACI score: 0.15 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Lysine--tRNA ligase
    Species: Homo sapiens [TaxId:9606]
    Gene: KARS, KIAA0070
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15046
      • conflict (231)
      • conflict (252)
      • conflict (268)
    Domains in SCOPe 2.05: d4ycwa1, d4ycwa2
  • Chain 'B':
    Compound: Lysine--tRNA ligase
    Species: Homo sapiens [TaxId:9606]
    Gene: KARS, KIAA0070
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15046
      • conflict (231)
      • conflict (252)
      • conflict (268)
    Domains in SCOPe 2.05: d4ycwb1, d4ycwb2
  • Chain 'C':
    Compound: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
    Species: Homo sapiens [TaxId:9606]
    Gene: AIMP2, JTV1, PRO0992
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
    Species: Homo sapiens [TaxId:9606]
    Gene: AIMP2, JTV1, PRO0992
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: Lysine--tRNA ligase
    Species: Homo sapiens [TaxId:9606]
    Gene: KARS, KIAA0070
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15046
      • conflict (231)
      • conflict (252)
      • conflict (268)
    Domains in SCOPe 2.05: d4ycwe1, d4ycwe2
  • Chain 'F':
    Compound: Lysine--tRNA ligase
    Species: Homo sapiens [TaxId:9606]
    Gene: KARS, KIAA0070
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15046
      • conflict (231)
      • conflict (252)
      • conflict (268)
    Domains in SCOPe 2.05: d4ycwf1, d4ycwf2
  • Chain 'G':
    Compound: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
    Species: Homo sapiens [TaxId:9606]
    Gene: AIMP2, JTV1, PRO0992
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
    Species: Homo sapiens [TaxId:9606]
    Gene: AIMP2, JTV1, PRO0992
    Database cross-references and differences (RAF-indexed):
  • Heterogens: LYS, KRS, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4ycwA (A:)
    msvdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkv
    agrihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnp
    gktkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirs
    kiityirsfldelgfleietpmmniipggavakpfityhneldmnlymriatelyhkmlv
    vggidrvyeigrvfrnegidlthnpeftscefymayadyhdlmeitekmvsgmvkhitgs
    ykvtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicv
    akavecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfel
    fvmkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwg
    mgidrvamfltdsnnikevllfpamkpedkken
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ycwA (A:)
    dpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkvagr
    ihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnpgkt
    kkgelsiipyeitllspclhmlphllkdketryrqryldlilndfvrqkfiirskiityi
    rsfldelgfleietpmmniipggavakpfityhneldmnlymriatelyhkmlvvggidr
    vyeigrvfrnegidlthnpeftscefymayadyhdlmeitekmvsgmvkhitgsykvtyh
    pdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicvakavec
    ppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfelfvmkke
    icnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwgmgidrv
    amfltdsnnikevllfpamkp
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4ycwB (B:)
    msvdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkv
    agrihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnp
    gktkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirs
    kiityirsfldelgfleietpmmniipggavakpfityhneldmnlymriatelyhkmlv
    vggidrvyeigrvfrnegidlthnpeftscefymayadyhdlmeitekmvsgmvkhitgs
    ykvtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicv
    akavecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfel
    fvmkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwg
    mgidrvamfltdsnnikevllfpamkpedkken
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ycwB (B:)
    dpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkvagr
    ihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnpgkt
    kkgelsiipyeitllspclhmlphllkdketryrqryldlilndfvrqkfiirskiityi
    rsfldelgfleietpmmniipggavakpfityhneldmnlymriatelyhkmlvvggidr
    vyeigrvfrnegidlthnpeftscefymayadyhdlmeitekmvsgmvkhitgsykvtyh
    pdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicvakavec
    ppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfelfvmkke
    icnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwgmgidrv
    amfltdsnnikevllfpamkp
    

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >4ycwE (E:)
    msvdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkv
    agrihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnp
    gktkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirs
    kiityirsfldelgfleietpmmniipggavakpfityhneldmnlymriatelyhkmlv
    vggidrvyeigrvfrnegidlthnpeftscefymayadyhdlmeitekmvsgmvkhitgs
    ykvtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicv
    akavecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfel
    fvmkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwg
    mgidrvamfltdsnnikevllfpamkpedkken
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ycwE (E:)
    dpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkvagr
    ihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnpgkt
    kkgelsiipyeitllspclhmlphldketryrqryldlilndfvrqkfiirskiityirs
    fldelgfleietpmmniipggavakpfityhneldmnlymriatelyhkmlvvggidrvy
    eigrvfrnegidlthnpeftscefymayadyhdlmeitekmvsgmvkhitgsykvtyhpd
    gpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicvakavecpp
    prttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfelfvmkkeic
    naytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwgmgidrvam
    fltdsnnikevllfpamkp
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >4ycwF (F:)
    msvdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkv
    agrihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnp
    gktkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirs
    kiityirsfldelgfleietpmmniipggavakpfityhneldmnlymriatelyhkmlv
    vggidrvyeigrvfrnegidlthnpeftscefymayadyhdlmeitekmvsgmvkhitgs
    ykvtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicv
    akavecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfel
    fvmkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwg
    mgidrvamfltdsnnikevllfpamkpedkken
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ycwF (F:)
    dpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkvagr
    ihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnpgkt
    kkgelsiipyeitllspclhmlphldketryrqryldlilndfvrqkfiirskiityirs
    fldelgfleietpmmniipggavakpfityhneldmnlymriatelyhkmlvvggidrvy
    eigrvfrnegidlthnpeftscefymayadyhdlmeitekmvsgmvkhitgsykvtyhpd
    gpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicvakaecppp
    rttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfelfvmkkeicn
    aytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwgmgidrvamf
    ltdsnnikevllfpamkp
    

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.