PDB entry 5dkv

View 5dkv on RCSB PDB site
Description: Crystal Structure of an ABC transporter Solute Binding Protein from Agrobacterium vitis(Avis_5339, TARGET EFI-511225) bound with alpha-D-Tagatopyranose
Class: sugar binding protein
Keywords: Solute Binding Protein, ENZYME FUNCTION INITIATIVE, EFI, Structural Genomics, SUGAR BINDING PROTEIN
Deposited on 2015-09-04, released 2015-09-30
The last revision prior to the SCOPe 2.06 freeze date was dated 2015-09-30, with a file datestamp of 2015-09-25.
Experiment type: XRAY
Resolution: 1.68 Å
R-factor: N/A
AEROSPACI score: 0.41 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: ABC transporter substrate binding protein (Ribose)
    Species: Agrobacterium vitis (strain S4 / ATCC BAA-846) [TaxId:311402]
    Gene: rbsB, Avi_5339
    Database cross-references and differences (RAF-indexed):
    • Uniprot B9K0T2 (23-323)
      • expression tag (21-22)
    Domains in SCOPe 2.06: d5dkva1, d5dkva2
  • Chain 'B':
    Compound: ABC transporter substrate binding protein (Ribose)
    Species: Agrobacterium vitis (strain S4 / ATCC BAA-846) [TaxId:311402]
    Gene: rbsB, Avi_5339
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5dkvb_
  • Chain 'C':
    Compound: ABC transporter substrate binding protein (Ribose)
    Species: Agrobacterium vitis (strain S4 / ATCC BAA-846) [TaxId:311402]
    Gene: rbsB, Avi_5339
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5dkvc_
  • Chain 'D':
    Compound: ABC transporter substrate binding protein (Ribose)
    Species: Agrobacterium vitis (strain S4 / ATCC BAA-846) [TaxId:311402]
    Gene: rbsB, Avi_5339
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5dkvd_
  • Heterogens: T6T, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5dkvA (A:)
    mhhhhhhssgvdlgtenlyfqsmenkkfrialipglttdafyitmhkgaeaaaaaigaqi
    ifqgapdfnpvtqvpvldaviakkpdailiaptdttqlvqplkkaadagipmitvdtfig
    tgdyqtgagdgdfplsyiasdnvlggeiaarslalaigdkgkvyvsnvkpgvsttdqreq
    gfksemakhpgitvletqfndndankaasqlqavyarnpdlagvfganlfsglgsangvq
    qagqsgtikvvafdapgsvvdnlksglidfaiaqhpaeigyygvisayahltgqsiptki
    gtgftvinksnvtdpavarfiyae
    

    Sequence, based on observed residues (ATOM records): (download)
    >5dkvA (A:)
    smenkkfrialipglttdafyitmhkgaeaaaaaigaqiifqgapdfnpvtqvpvldavi
    akkpdailiaptdttqlvqplkkaadagipmitvdtfigtgdyqtgagdgdfplsyiasd
    nvlggeiaarslalaigdkgkvyvsnvkpgvsttdqreqgfksemakhpgitvletqfnd
    ndankaasqlqavyarnpdlagvfganlfsglgsangvqqagqsgtikvvafdapgsvvd
    nlksglidfaiaqhpaeigyygvisayahltgqsiptkigtgftvinksnvtdpavarfi
    yae
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5dkvB (B:)
    mhhhhhhssgvdlgtenlyfqsmenkkfrialipglttdafyitmhkgaeaaaaaigaqi
    ifqgapdfnpvtqvpvldaviakkpdailiaptdttqlvqplkkaadagipmitvdtfig
    tgdyqtgagdgdfplsyiasdnvlggeiaarslalaigdkgkvyvsnvkpgvsttdqreq
    gfksemakhpgitvletqfndndankaasqlqavyarnpdlagvfganlfsglgsangvq
    qagqsgtikvvafdapgsvvdnlksglidfaiaqhpaeigyygvisayahltgqsiptki
    gtgftvinksnvtdpavarfiyae
    

    Sequence, based on observed residues (ATOM records): (download)
    >5dkvB (B:)
    nkkfrialipglttdafyitmhkgaeaaaaaigaqiifqgapdfnpvtqvpvldaviakk
    pdailiaptdttqlvqplkkaadagipmitvdtfigtgdyqtgagdgdfplsyiasdnvl
    ggeiaarslalaigdkgkvyvsnvkpgvsttdqreqgfksemakhpgitvletqfndnda
    nkaasqlqavyarnpdlagvfganlfsglgsangvqqagqsgtikvvafdapgsvvdnlk
    sglidfaiaqhpaeigyygvisayahltgqsiptkigtgftvinksnvtdpavarfiyae
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5dkvC (C:)
    mhhhhhhssgvdlgtenlyfqsmenkkfrialipglttdafyitmhkgaeaaaaaigaqi
    ifqgapdfnpvtqvpvldaviakkpdailiaptdttqlvqplkkaadagipmitvdtfig
    tgdyqtgagdgdfplsyiasdnvlggeiaarslalaigdkgkvyvsnvkpgvsttdqreq
    gfksemakhpgitvletqfndndankaasqlqavyarnpdlagvfganlfsglgsangvq
    qagqsgtikvvafdapgsvvdnlksglidfaiaqhpaeigyygvisayahltgqsiptki
    gtgftvinksnvtdpavarfiyae
    

    Sequence, based on observed residues (ATOM records): (download)
    >5dkvC (C:)
    kfrialipglttdafyitmhkgaeaaaaaigaqiifqgapdfnpvtqvpvldaviakkpd
    ailiaptdttqlvqplkkaadagipmitvdtfigtgdyqtgagdgdfplsyiasdnvlgg
    eiaarslalaigdkgkvyvsnvkpgvsttdqreqgfksemakhpgitvletqfndndank
    aasqlqavyarnpdlagvfganlfsglgsangvqqagqsgtikvvafdapgsvvdnlksg
    lidfaiaqhpaeigyygvisayahltgqsiptkigtgftvinksnvtdpavarfiyae
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5dkvD (D:)
    mhhhhhhssgvdlgtenlyfqsmenkkfrialipglttdafyitmhkgaeaaaaaigaqi
    ifqgapdfnpvtqvpvldaviakkpdailiaptdttqlvqplkkaadagipmitvdtfig
    tgdyqtgagdgdfplsyiasdnvlggeiaarslalaigdkgkvyvsnvkpgvsttdqreq
    gfksemakhpgitvletqfndndankaasqlqavyarnpdlagvfganlfsglgsangvq
    qagqsgtikvvafdapgsvvdnlksglidfaiaqhpaeigyygvisayahltgqsiptki
    gtgftvinksnvtdpavarfiyae
    

    Sequence, based on observed residues (ATOM records): (download)
    >5dkvD (D:)
    kfrialipglttdafyitmhkgaeaaaaaigaqiifqgapdfnpvtqvpvldaviakkpd
    ailiaptdttqlvqplkkaadagipmitvdtfigtgdyqtgagdgdfplsyiasdnvlgg
    eiaarslalaigdkgkvyvsnvkpgvsttdqreqgfksemakhpgitvletqfndndank
    aasqlqavyarnpdlagvfganlfsglgsangvqqagqsgtikvvafdapgsvvdnlksg
    lidfaiaqhpaeigyygvisayahltgqsiptkigtgftvinksnvtdpavarfiyae